Structural basis for the activation process of [NiFe] hydrogenase from D.vulgaris Miyazaki F
Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Periplasmic [NiFe] hydrogenase small subunit | A [auth S] | 267 | Nitratidesulfovibrio vulgaris str. 'Miyazaki F | Mutation(s): 0  EC: 1.12.2.1 | ![]() |
UniProt | |||||
Find proteins for P21853 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore P21853  Go to UniProtKB:  P21853 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P21853 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Periplasmic [NiFe] hydrogenase large subunit | B [auth L] | 534 | Nitratidesulfovibrio vulgaris str. 'Miyazaki F | Mutation(s): 2  EC: 1.12.2.1 | ![]() |
UniProt | |||||
Find proteins for P21852 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore P21852  Go to UniProtKB:  P21852 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P21852 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 5 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SF4 Query on SF4 | C [auth S], D [auth S] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N | |||
F3S Query on F3S | E [auth S] | FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N | |||
NFC Query on NFC | I [auth L] | NI-FE ACTIVE CENTER A-FORM C3 H2 Fe N Ni O4 CIUCFLVMTAQNSJ-UHFFFAOYSA-N | |||
MPD Query on MPD | F [auth S], G [auth S] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N | |||
MG Query on MG | H [auth L] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
CSO Query on CSO | B [auth L] | L-PEPTIDE LINKING | C3 H7 N O3 S | CYS |
Length ( Å ) | Angle ( ˚ ) |
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a = 98.227 | α = 90 |
b = 126.261 | β = 90 |
c = 66.44 | γ = 90 |
Software Name | Purpose |
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SHELX | model building |
SHELXL-97 | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
CNS | phasing |