Primary Citation PubMed: 9737845
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HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.
(2009) PLoS One 4
PubMed: 19693270 | PubMedCentral: PMC2724740 | DOI: 10.1371/journal.pone.0006701
PDB ID in NMR PDB ID in X-ray Length RMSD (Å) a Resolution (Å) b N NOE c 1vre 1jf4 147 1.333 1.40 2097 1jor 1ey4 134 2.792 1.60 1596 1bla 1bfg 126 0.976 1.60 2196 1kdf 1msi 64 0.826 1.... 5 1197 1ikm 3il8 68 4.733 2.00 892 3gbl 1pgb 56 0.541 1.92 671 3ci2 2ci2 63 1.262 2.00 944 1eq0 1hka 158 3.182 1.50 2856 3phy 1gsv 121 1.932 1.75 1145 1r63 1r69 63 0.764 2.00 531 1jnj 1lds 96 3.450 1.80 696 3mef 1mjc 68 1.529 2.00 421 1jv9 6pti 55 0.690 1.70 534 a RMSD of all the heavy atoms after superposing the NMR and the X-ray structures.
Publication Year: 2009
Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.
(2014) PLoS Comput Biol 10
PubMed: 25356903 | PubMedCentral: PMC4214557 | DOI: 10.1371/journal.pcbi.1003797
The structure of the dark pG state has been determined by NMR spectroscopy  , and the resulting structures are in the Protein Data Bank (PDB)  , with PDB ID: 3PHY.
g003 Figure 3 Configuration from a) pG state (PDB ID: 3PHY), b) experimental signaling state of WT-PYP (PDB ID: 2XK6), c) experimental signaling state of Δ25 (PDB ID: 1XFQ), d) representative configuration from our pB ensemble.
These fluctuations are computed by first aligning the corresponding C α 's to the last 100 residues of the pG configuration (model 11 of PDB ID: 3PHY  ), and then calculating the displacement of the C α 's from that pG configuration.
Publication Year: 2014
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