Biophysical highlights from 54 years of macromolecular crystallography

Biophysical Journal

Volumn 106, Issue 3, 2014, Pages 510-525

  Richardson, Jane S ^a   Richardson, David C ^a  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; HUMAN; METHODOLOGY; MOLECULAR GENETICS; PROTEIN CONFORMATION; REVIEW; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; CRYSTALLOGRAPHY, X-RAY; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEINS;

EID: 84893506536     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.01.001     Document Type: Review

References (147)

1. J.C. Kendrew, and R.E. Dickerson V.C. Shore Structure of myoglobin: a three-dimensional Fourier synthesis at 2 Å resolution Nature 185 1960 422 427
2. H. Frauenfelder, B.H. McMahon, and P.W. Fenimore Myoglobin: the hydrogen atom of biology and a paradigm of complexity Proc. Natl. Acad. Sci. USA 100 2003 8615 8617
3. J.C. Hanson, and B.P. Schoenborn Real space refinement of neutron diffraction data from sperm whale carbonmonoxymyoglobin J. Mol. Biol. 153 1981 117 146
4. J.Z. Ruscio, and D. Kumar A.V. Onufriev Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin Proc. Natl. Acad. Sci. USA 105 2008 9204 9209
5. M.F. Perutz, and M.G. Rossmann A.C.T. North Structure of hemoglobin: a three-dimensional Fourier synthesis at 5.5-Å resolution, obtained by x-ray analysis Nature 185 1960 416 422
6. M.F. Perutz, and F.S. Mathews An x-ray study of azide Met-hemoglobin J. Mol. Biol. 21 1966 199 202
7. C.C.F. Blake, and D.F. Koenig V.R. Sarma Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Ångstrom resolution Nature 206 1965 757 761
8. A. Warshel, and M. Levitt Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme J. Mol. Biol. 103 1976 227 249
9. R. Diamond Real-space refinement of the structure of hen egg-white lysozyme J. Mol. Biol. 82 1974 371 391
10. S. Boutet, and L. Lomb I. Schlichting High-resolution protein structure determination by serial femtosecond crystallography Science 337 2012 362 364
11. D. Shi, and B.L. Nannenga T. Gonen Three-dimensional electron crystallography of protein microcrystals Elife 2 2013 e01345
12. G. Kartha, J. Bello, and D. Harker Tertiary structure of ribonuclease Nature 213 1967 862 865
13. H.W. Wyckoff, and K.D. Hardman F.M. Richards The structure of ribonuclease-S at 3.5 Å resolution J. Biol. Chem. 242 1967 3984 3988
14. B.W. Matthews, and P.B. Sigler D.M. Blow Three-dimensional structure of tosyl-α-chymotrypsin Nature 214 1967 652 656
15. S.T. Freer, and J. Kraut N.H. Xuong Chymotrypsinogen: 2.5-Ångstrom crystal structure, comparison with α-chymotrypsin, and implications for zymogen activation Biochemistry 9 1970 1997 2009
16. H. Fehlhammer, and W. Bode The refined crystal structure of bovine β-trypsin at 1.8 Å resolution. II. Crystallographic refinement, calcium binding site, benzamidine binding site and active site at pH 7.0 J. Mol. Biol. 98 1975 693 697
17. W.N. Lipscomb, and J.A. Hartsuck J.C. Coppola The structure of carboxypeptidase A, VII. The 2.0-Å resolution studies of the enzyme and of its complex with glycyltyrosine, and mechanistic deductions Brookhaven Symposia in Biology: Structure, Function, and Evolution in Proteins No. 21 1969 Brookhaven National Laboratory Upton, NY 24 90
18. C.S. Wright, R.A. Alden, and J. Kraut Structure of subtilisin BPN′ at 2.5 Ångström resolution Nature 221 1969 235 242
19. J.A. Wells, and D.A. Estell Subtilisin - an enzyme designed to be engineered Trends Biochem. Sci. 13 1988 291 297
20. M.J. Adams, and G.C. Ford A.J. Wonacott Structure of lactate dehydrogenase at 2-8 Å resolution Nature 227 1970 1098 1103
21. R. Huber, and D. Kukla H. Formanek The basic trypsin inhibitor of bovine pancreas. I. Structure analysis and conformation of the polypeptide chain Naturwissenschaften 57 1970 389 392
22. A. Ruehlmann, and D. Kukla R. Huber Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. Crystal structure determination and stereochemistry of the contact region J. Mol. Biol. 77 1973 417 436
23. A. Dubs, G. Wagner, and K. Wuthrich Individual assignments of amide proton resonances in the proton NMR spectrum of the basic pancreatic trypsin inhibitor Biochem. Biophys. Acta 577 1979 177 194
24. J.A. McCammon, and M. Karplus Dynamics of tyrosine ring rotations in a globular protein Biopolymers 19 1980 1375 1405
25. J.R. Herriott, and L.C. Sieker W. Lovenberg Structure of rubredoxin: an x-ray study to 2.5 Å resolution J. Mol. Biol. 50 1970 391 406
26. K.D. Watenpaugh, L.C. Sieker, and L.H. Jensen Crystallographic refinement of rubredoxin at 1 × 2 Å degrees resolution J. Mol. Biol. 138 1980 615 633
27. T.L. Blundell, and J.F. Cutfield M. Vijayan Atomic positions in rhombohedral 2-zinc insulin crystals Nature 231 1971 506 511
28. A. Arnone, and C.J. Bier A. Yonath A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing J. Biol. Chem. 246 1971 2302 2316
29. P.W. Tucker, E.E. Hazen Jr., and F.A. Cotton Staphylococcal nuclease reviewed: a prototypic study in contemporary enzymology. IV. The nuclease as a model for protein folding Mol. Cell. Biochem. 23 1979 131 141
30. D. Shortle Staphylococcal nuclease: a showcase of m-value effects Adv. Protein Chem. 46 1995 217 247
31. R.E. Dickerson, and T. Takano E. Margoliash Ferricytochrome c. I. General features of the horse and bonito proteins at 2.8 Å resolution J. Biol. Chem. 246 1971 1511 1535
32. H. Pelletier, and J. Kraut Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c Science 258 1992 1748 1755
33. B.W. Matthews, and S.J. Remington The three-dimensional structure of the lysozyme from bacteriophage T4 Proc. Natl. Acad. Sci. USA 71 1974 4178 4182
34. W.A. Baase, and L. Liu B.W. Matthews Lessons from the lysozyme of phage T4 Protein Sci. 19 2010 631 641
35. R.J. Poljak, and L.M. Amzel F. Saul The three-dimensional structure of the Fab′ fragment of a human myeloma immunoglobulin at 2.0-Ångstrom resolution Proc. Natl. Acad. Sci. USA 71 1974 3440 3444
36. O. Epp, and E.E. Lattman W. Palm The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0-Å resolution Biochemistry 14 1975 4943 4952
37. C. Chothia, and A.M. Lesk Canonical structures for the hypervariable regions of immunoglobulins J. Mol. Biol. 196 1987 901 917
38. B. North, A. Lehmann, and R.L. Dunbrack Jr. A new clustering of antibody CDR loop conformations J. Mol. Biol. 406 2011 228 256
39. J.S. Richardson, and K.A. Thomas D.C. Richardson Crystal structure of bovine Cu,Zn superoxide dismutase at 3 Å resolution: chain tracing and metal ligands Proc. Natl. Acad. Sci. USA 72 1975 1349 1353
40. J.S. Richardson β-Sheet topology and the relatedness of proteins Nature 268 1977 495 500
41. J.L. Sussman, and S.-H. Kim Three-dimensional structure of a transfer RNA in two crystal forms Science 192 1976 853 858
42. A. Jack, J.E. Ladner, and A. Klug Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5Å resolution J. Mol. Biol. 108 1976 619 649
43. I. Tinoco Jr., and R.L. Gonzalez Jr. Biological mechanisms, one molecule at a time Genes Dev. 25 2011 1205 1231
44. J.A. Dunkle, and L. Wang J.H. Cate Structures of the bacterial ribosome in classical and hybrid states of tRNA binding Science 332 2011 981 984
45. D.W. Banner, and A. Bloomer I.A. Wilson Atomic coordinates for triose phosphate isomerase from chicken muscle Biochem. Biophys. Res. Commun. 72 1976 146 155
46. E. Lolis, and G.A. Petsko Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-Å resolution: implications for catalysis Biochemistry 29 1990 6619 6625
47. S.C. Harrison, and A.J. Olson G. Bricogne Tomato bushy stunt virus at 2.9 Å resolution Nature 276 1978 368 373
48. C. Abad-Zapatero, and S.S. Abdel-Meguid T. Tsukihara Structure of Southern bean mosaic virus at 2.8 Å resolution Nature 286 1980 33 39
49. H.R. Drew, and R.M. Wing R.E. Dickerson Structure of a B-DNA dodecamer: conformation and dynamics Proc. Natl. Acad. Sci. USA 78 1981 2179 2183
50. W.A. Hendrickson, and M.M. Teeter Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulfur Nature 290 1981 107 113
51. C. Jelsch, M.M. Teeter, and C. Lecomte Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin Proc. Natl. Acad. Sci. USA 97 2000 3171 3176
52. A. Schmidt, and M. Teeter V.S. Lamzin Crystal structure of small protein crambin at 0.48 Å resolution Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67 2011 424 428
53. J.C.-H. Chen, and Z. Fisher P. Langan Room-temperature ultrahigh-resolution time-of-flight neutron and x-ray diffraction studies of H/D-exchanged crambin Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 2012 119 123
54. Y.S. Babu, and J.S. Sack W.J. Cook Three-dimensional structure of calmodulin Nature 315 1985 37 40
55. O. Herzberg, and M.N.G. James Structure of the calcium regulatory muscle protein troponin-C at 2.8 Å resolution Nature 313 1985 653 659
56. M. Ikura, and G.M. Clore A. Bax Solution structure of a calmodulin-target peptide complex by multidimensional NMR Science 256 1992 632 638
57. M.E. Wall, J.B. Clarage, and G.N. Phillips Jr. Motions of calmodulin characterized using both Bragg and diffuse x-ray scattering Structure 5 1997 1599 1612
58. D.L. Ollis, and P. Brick T.A. Steitz Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP Nature 313 1985 762 766
59. J.R. Kiefer, and C. Mao L.S. Beese Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal Nature 391 1998 304 307
60. J. Deisenhofer, and O. Epp H. Michel Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3Å resolution Nature 318 1985 618 624
61. Y. Takeda, and J.G. Kim B.W. Matthews Different interactions used by Cro repressor in specific and nonspecific DNA binding J. Biol. Chem. 261 1986 8608 8616
62. S.R. Jordan, and C.O. Pabo Structure of the λ-complex at 2.5 Å resolution: details of the repressor-operator interactions Science 242 1988 893 899
63. Z. Otwinowski, and R.W. Schevitz P.B. Sigler Crystal structure of Trp repressor/operator complex at atomic resolution Nature 335 1988 321 329
64. S.C. Schultz, G.C. Shields, and T.A. Steitz Crystal structure of a CAP-DNA complex: the DNA is bent by 90 Science 253 1991 1001 1007
65. N.P. Pavletich, and C.O. Pabo Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å Science 252 1991 809 817
66. P.J. Bjorkman, and M.A. Saper D.C. Wiley Structure of the human class I histocompatibility antigen, HLA-A2 Nature 329 1987 506 512
67. S. Vijay-Kumar, C.E. Bugg, and W.J. Cook Structure of ubiquitin refined at 1.8 Å resolution J. Mol. Biol. 194 1987 531 544
68. B. Richter, and J. Gsponer M. Vendruscolo The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins J. Biomol. NMR 37 2007 117 135
69. R. Henderson, and J.M. Baldwin K.H. Downing Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy J. Mol. Biol. 213 1990 899 929
70. N. Grigorieff, and T.A. Ceska R. Henderson Electron-crystallographic refinement of the structure of bacteriorhodopsin J. Mol. Biol. 259 1996 393 421
71. E.K. O'Shea, and J.D. Klemm T. Alber X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil Science 254 1991 539 544
72. P.B. Harbury, and T. Zhang T. Alber A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants Science 262 1993 1401 1407
73. M.D. Yoder, N.T. Keen, and F. Jurnak New domain motif: the structure of pectate lyase C, a secreted plant virulence factor Science 260 1993 1503 1507
74. C. Kisker, and H. Schindelin D.C. Rees A left-hand β-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila EMBO J. 15 1996 2323 2330
75. J. Bella, and M. Eaton H.M. Berman Crystal and molecular structure of a collagen-like peptide at 1.9 Å resolution Science 266 1994 75 81
76. A.M. Buckle, G. Schreiber, and A.R. Fersht Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-Å resolution Biochemistry 33 1994 8878 8889
77. T. Wang, and S. Tomic R.C. Wade How optimal are the binding energetics of barnase and barstar? Biophys. J. 87 2004 1618 1630
78. 1-ATPase from bovine heart mitochondria Nature 370 1994 621 628
79. 2 Cell 83 1995 1047 1058
80. D.G. Lambright, and J. Sondek P.B. Sigler The 2.0 Å crystal structure of a heterotrimeric G protein Nature 379 1996 311 319
81. R.J. Lefkowitz Historical review: a brief history and personal retrospective of seven-transmembrane receptors Trends Pharmacol. Sci. 25 2004 413 422
82. M. Ormö, and A.B. Cubitt S.J. Remington Crystal structure of the Aequorea victoria green fluorescent protein Science 273 1996 1392 1395
83. P.D. Jeffrey, and A.A. Russo N.P. Pavletich Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex Nature 376 1995 313 320
84. A.A. Russo, P.D. Jeffrey, and N.P. Pavletich Structural basis of cyclin-dependent kinase activation by phosphorylation Nat. Struct. Biol. 3 1996 696 700
85. F.J. Kull, and E.P. Sablin R.D. Vale Crystal structure of the kinesin motor domain reveals a structural similarity to myosin Nature 380 1996 550 555
86. F. Kozielski, and S. Sack E. Mandelkow The crystal structure of dimeric kinesin and implications for microtubule-dependent motility Cell 91 1997 985 994
87. C.L. Asbury, A.N. Fehr, and S.M. Block Kinesin moves by an asymmetric hand-over-hand mechanism Science 302 2003 2130 2134
88. 7 chaperonin complex Nature 388 1997 741 750
89. K. Luger, and A.W. Mäder T.J. Richmond Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature 389 1997 251 260
90. K. Luger, M.L. Dechassa, and D.J. Tremethick New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat. Rev. Mol. Cell Biol. 13 2012 436 447
91. B.L. Golden, and A.R. Gooding T.R. Cech A preorganized active site in the crystal structure of the Tetrahymena ribozyme Science 282 1998 259 264
92. M.R. Redinbo, and L. Stewart W.G.J. Hol Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA Science 279 1998 1504 1513
93. J.M. Berger, and S.J. Gamblin J.C. Wang Structure and mechanism of DNA topoisomerase II Nature 379 1996 225 232
94. E. Nogales, S.G. Wolf, and K.H. Downing Structure of the α β tubulin dimer by electron crystallography Nature 391 1998 199 203
95. E.S. Nogales, and H.-W. Wang Structural mechanisms underlying nucleotide-dependent self-assembly of tubulin and its relatives Curr. Opin. Struct. Biol. 16 2006 221 229
96. + conduction and selectivity Science 280 1998 69 77
97. D.N. Gopaul, F. Guo, and G.D. van Duyne Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination EMBO J. 17 1998 4175 4187
98. M. Ariyoshi, and T. Nishino K. Morikawa Crystal structure of the Holliday junction DNA in complex with a single RuvA tetramer Proc. Natl. Acad. Sci. USA 97 2000 8257 8262
99. J.M. Vargason, and P.S. Ho The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution J. Biol. Chem. 277 2002 21041 21049
100. N. Ban, and P. Nissen T.A. Steitz The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution Science 289 2000 905 920
101. A.P. Carter, and W.M. Clemons V. Ramakrishnan Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics Nature 407 2000 340 348
102. F. Schluenzen, and A. Tocilj A. Yonath Structure of functionally activated small ribosomal subunit at 3.3 Ångstroms resolution Cell 102 2000 615 623
103. B.S. Schuwirth, and M.A. Borovinskaya J.H. Cate Structures of the bacterial ribosome at 3.5 Å resolution Science 310 2005 827 834
104. M.C. Sousa, and C.B. Trame D.B. McKay Crystal and solution structures of an HslUV protease-chaperone complex Cell 103 2000 633 643
105. D. Gai, and R. Zhao X.S. Chen Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen Cell 119 2004 47 60
106. B.A. Kelch, and D.L. Makino J. Kuriyan How a DNA polymerase clamp loader opens a sliding clamp Science 334 2011 1675 1680
107. X. Wang, and J. McLachlan T.M.T. Hall Modular recognition of RNA by a human pumilio-homology domain Cell 110 2002 501 512
108. B. Kobe, and J. Deisenhofer A structural basis of the interactions between leucine-rich repeats and protein ligands Nature 374 1995 183 186
109. P. Michaely, and D.R. Tomchick R.G.W. Anderson Crystal structure of a 12 ANK repeat stack from human ankyrinR EMBO J. 21 2002 6387 6396
110. M.A. Kramer, and S.K. Wetzel M.G. Grütter Structural determinants for improved stability of designed ankyrin repeat proteins with a redesigned C-capping module J. Mol. Biol. 404 2010 381 391
111. B. Kuhlman, and G. Dantas D. Baker Design of a novel globular protein fold with atomic-level accuracy Science 302 2003 1364 1368
112. S. Raman, and O.F. Lange D. Baker NMR structure determination for larger proteins using backbone-only data Science 327 2010 1014 1018
113. F. DiMaio, and M.D. Tyka D. Baker Refinement of protein structures into low-resolution density maps using ROSETTA J. Mol. Biol. 392 2009 181 190
114. P.D. Adams, and D. Baker T.C. Terwilliger Advances, interactions, and future developments in the CNS, PHENIX, and ROSETTA structural biology software systems Annu. Rev. Biophys 42 2013 265 287
115. S. Ye, and I. Vakonakis J.C. Sacchettini Crystal structure of circadian clock protein KaiA from Synechococcus elongatus J. Biol. Chem. 279 2004 20511 20518
116. R.G. Garces, and N. Wu E.F. Pai Anabaena circadian clock proteins KaiA and KaiB reveal a potential common binding site to their partner KaiC EMBO J. 23 2004 1688 1698
117. R. Pattanayek, and D.R. Williams M. Egli Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods EMBO J. 25 2006 2017 2028
118. R.T. Batey, S.D. Gilbert, and R.K. Montange Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine Nature 432 2004 411 415
119. A. Serganov, and Y.R. Yuan D.J. Patel Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs Chem. Biol. 11 2004 1729 1741
120. Q. Liu, J.C. Greimann, and C.D. Lima Reconstitution, activities, and structure of the eukaryotic RNA exosome Cell 127 2006 1223 1237
121. 2-adrenergic G protein-coupled receptor Science 318 2007 1258 1265
122. S.G. Rasmussen, and B.T. DeVree B.K. Kobilka Crystal structure of the β2 adrenergic receptor-Gs protein complex Nature 477 2011 549 555
123. E.M. Landau, and J.P. Rosenbusch Lipidic cubic phases: a novel concept for the crystallization of membrane proteins Proc. Natl. Acad. Sci. USA 93 1996 14532 14535
124. H. Tanaka, and K. Kato T. Tsukihara The structure of rat liver vault at 3.5 Ångstrom resolution Science 323 2009 384 388
125. A. Casañas, and J. Querol-Audí I. Fita New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach Acta Crystallogr. D Biol. Crystallogr. 69 2013 1054 1061
126. H.N. Chapman, and P. Fromme J.C. Spence Femtosecond x-ray protein nanocrystallography Nature 470 2011 73 77
127. J. Kern, and R. Alonso-Mori V.K. Yachandra Room temperature femtosecond x-ray diffraction of photosystem II microcrystals Proc. Natl. Acad. Sci. USA 109 2012 9721 9726
128. L. Redecke, and K. Nass H.N. Chapman Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an x-ray laser Science 339 2013 227 230
129. F.C. Bernstein, and T.F. Koetzle M.J. Tasumi The Protein Data Bank: a computer-based archival file for macromolecular structures J. Mol. Biol. 112 1977 535 542
130. J.S. Richardson The anatomy and taxonomy of protein structure Adv. Protein Chem. 34 1981 167 339
131. D.C. Richardson, and J.S. Richardson Mage, probe, and kinemages M.G. Rossmann, E. Arnold, IUCr's International Tables of Crystallography, Vol. F: Crystallography of Biological Macromolecules 2001 Kluwer Academic Press Dordrecht, the Netherlands
132. V.B. Chen, I.W. Davis, and D.C. Richardson KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program Protein Sci. 18 2009 2403 2409
133. Commons, Wikimedia. http://commons.wikimedia.org/wiki/User:Dcrjsr.
134. Goodsell, D. Molecule of the Month. http://www.rcsb.org/pdb/101/motm- archive.do.
135. M. Tarini, P. Cignoni, and C. Montani Ambient occlusion and edge cueing to enhance real time molecular visualization IEEE Trans. Vis. Comput. Graph. 12 2006 1237 1244
136. Wikipedia. English. http://en.wikipedia/wiki/List-of-biophysically- important-macromolecular-crystal
137. S.K. Burley PDB40: the Protein Data Bank celebrates its 40th birthday Biopolymers 99 2013 165 169
138. L. Sawyer, and D.M. Shotton H.C. Watson The atomic structure of crystalline porcine pancreatic elastase at 2.5 Å resolution: comparisons with the structure of α-chymotrypsin J. Mol. Biol. 118 1978 137 208
139. X.J. Zhang, and B.W. Matthews Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme Protein Sci. 3 1994 1031 1039
140. R.H. Jacobson, and M. Matsumura B.W. Matthews Structure of a stabilizing disulfide bridge mutant that closes the active-site cleft of T4 lysozyme Protein Sci. 1 1992 46 57
141. J.A. Tainer, and E.D. Getzoff D.C. Richardson Determination and analysis of the 2 Å-structure of copper, zinc superoxide dismutase J. Mol. Biol. 160 1982 181 217
142. H. Shi, and P.B. Moore The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited RNA 6 2000 1091 1105
143. 6-methyl-guanine lesions Proc. Natl. Acad. Sci. USA 103 2006 19701 19706
144. M.A. Saper, P.J. Bjorkman, and D.C. Wiley Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å resolution J. Mol. Biol. 219 1991 277 319
145. T.M. Iverson, and B.E. Alber D.C. Rees A closer look at the active site of γ-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila Biochemistry 39 2000 9222 9231
146. U. Schulze-Gahmen, H.L. De Bondt, and S.-H. Kim High-resolution crystal structures of human cyclin-dependent kinase 2 with and without ATP: bound waters and natural ligand as guides for inhibitor design J. Med. Chem. 39 1996 4540 4546
147. L. Brino, and A. Urzhumtsev D. Moras Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center J. Biol. Chem. 275 2000 9468 9475