1WUH | pdb_00001wuh

Three-Dimensional Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

PDB DOI: https://doi.org/10.2210/pdb1WUH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Mutation(s): Yes

Deposited: 2004-12-07 Released: 2005-12-07
Deposition Author(s): Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K., Higuchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.24 Å
R-Value Free:
0.157 (Depositor)
R-Value Work:
0.110 (Depositor)
R-Value Observed:
0.113 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

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.

Macromolecule Content

Total Structure Weight: 89.52 kDa
Atom Count: 7,108
Modeled Residue Count: 801
Deposited Residue Count: 801
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21853
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21852
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain D [auth S] SDF format, chain C [auth S] MOL2 format, chain D [auth S] MOL2 format, chain C [auth S] mmCIF format, chain D [auth S] mmCIF format, chain C [auth S]	C [auth S], D [auth S]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth S] Focus chain D [auth S]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain E [auth S] MOL2 format, chain E [auth S] mmCIF format, chain E [auth S]	E [auth S]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain E [auth S]
NFC Query on NFC Download:Ideal Coordinates CCD File SDF format, chain I [auth L] MOL2 format, chain I [auth L] mmCIF format, chain I [auth L]	I [auth L]	NI-FE ACTIVE CENTER A-FORM C₃ H₂ Fe N Ni O₄ CIUCFLVMTAQNSJ-UHFFFAOYSA-N		Interactions Focus chain I [auth L]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain F [auth S] SDF format, chain G [auth S] MOL2 format, chain F [auth S] MOL2 format, chain G [auth S] mmCIF format, chain F [auth S] mmCIF format, chain G [auth S]	F [auth S], G [auth S]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth S] Focus chain G [auth S]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth L] MOL2 format, chain H [auth L] mmCIF format, chain H [auth L]	H [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	B [auth L]	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.24 Å
R-Value Free: 0.157 (Depositor)
R-Value Work: 0.110 (Depositor)
R-Value Observed: 0.113 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.227	α = 90
b = 126.261	β = 90
c = 66.44	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-12-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-12-07
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2019-09-04
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary