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0004152433
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Tsukihara, T.; Shimokata, K.; Katayama, Y.; Shimada, H.; Muramoto, K.; Aoyama, H.; Mochizuki, M.; Shinzawa-Itoh, K.; Yamashita, E.; Yao, M.; Ishimura, Y.; Yoshikawa, S. Proc. Natl. Acad. Sci. USA. 2003, 100, 15304-15309.
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(a) Muramoto, K.; Hirata, K.; Shinzawa-Itoh, K.; Yoko-o, S.; Yamashita, E.; Aoyama, H.; Tsukihara, T.; Yoshikawa, S. Proc. Natl. Acad. Sci. USA. 2007, 104, 7881-7886.
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Yoshikawa, S.8
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26
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84906375775
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The RCSB Protein Data Bank (PDB: http://www.pdb.org/), PDB ID 2eij.
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(b) The RCSB Protein Data Bank (PDB: http://www.pdb.org/), PDB ID 2eij.
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27
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84906404437
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Codes used in the present work are based on Tokyo Ab initio Program Package (TAPP);
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(a) Codes used in the present work are based on Tokyo Ab initio Program Package (TAPP);
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28
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0000873095
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(b) Yamauchi, J.; Tsukada, M.; Watanabe, S.; Sugino, O. Phys. Rev. B. 1996, 54, 5586-5603.
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Yamauchi, J.1
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Watanabe, S.3
Sugino, O.4
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31
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4243943295
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Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868.
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Perdew, J.P.1
Burke, K.2
Ernzerhof, M.3
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34
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0345491105
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Lee, C.; Yang, W.; Parr, R. G. Phys. Rev.B 1988, 37, 785-789.
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Phys. Rev.B
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Lee, C.1
Yang, W.2
Parr, R.G.3
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35
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0001652762
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Hamprecht, F. A.; Cohen, A. J.; Tozer, D. J.; Handy, N. C. J. Chem. Phys. 1998, 109, 6264-6271.
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J. Chem. Phys
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Hamprecht, F.A.1
Cohen, A.J.2
Tozer, D.J.3
Handy, N.C.4
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36
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84906389709
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These DFT calculations have been conducted by using the CarrParrinello Molecular Dynamics code (CPMD, Copyright IBM Corp. 1990-2006, Copyright MPI fur Festkörperforschung Stuttgart 1997-2001.).
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These DFT calculations have been conducted by using the CarrParrinello Molecular Dynamics code (CPMD, Copyright IBM Corp. 1990-2006, Copyright MPI fur Festkörperforschung Stuttgart 1997-2001.).
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38
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84906389710
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2, and NFeO. The differences between our calculated results and the experimental and/or theoretical available data are 0.1 - 1.3%, assuring required accuracy in the present calculations.
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2, and NFeO. The differences between our calculated results and the experimental and/or theoretical available data are 0.1 - 1.3%, assuring required accuracy in the present calculations.
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39
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84906389711
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The positions of five terminal H atoms and the H in the hydroxyl group have been kept fixed, according to the CcO crystal structure
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The positions of five terminal H atoms and the H in the hydroxyl group have been kept fixed, according to the CcO crystal structure.
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40
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84906389708
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The geometry optimization has been performed until the forces become less than 5.1 × 10-2 eV/Å. During the calculations, the positions of the Cα atom and four terminal H atoms of the imidazole ligands and the C and H atoms in the hydroxyl group have been kept fixed, in accordance with the CcO X-ray structure, 37 The present heme b model has been constructed on the basis of the X-ray structure of the bovine cytochrome b 538 in a similar manner as in the case of the heme a. An orthorhombic supercell was obtained with the following sizes: a, 16.75 Å, b, 17.23 Å, and c, 20.53 Å. The DFT calculations have been performed in the plane-wave basis set with a cutoff energy of 80 Ry by using the PBE exchange-correlation functional and Troullier-Martins norm-conserving pseudopotentials
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38 in a similar manner as in the case of the heme a. An orthorhombic supercell was obtained with the following sizes: a ) 16.75 Å, b ) 17.23 Å, and c ) 20.53 Å. The DFT calculations have been performed in the plane-wave basis set with a cutoff energy of 80 Ry by using the PBE exchange-correlation functional and Troullier-Martins norm-conserving pseudopotentials.
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42
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84906375774
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The PDB ID is 1cyo
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(b) The PDB ID is 1cyo.
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43
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84906404436
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20 of the porphyrin (in accordance with 1-24 IUPAC numbering nomenclature) in heme b, whereas they are perpendicular each other in heme a.
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20 of the porphyrin (in accordance with 1-24 IUPAC numbering nomenclature) in heme b, whereas they are perpendicular each other in heme a.
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