1H0H | pdb_00001h0h

Tungsten containing Formate Dehydrogenase from Desulfovibrio Gigas

PDB DOI: https://doi.org/10.2210/pdb1H0H/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Megalodesulfovibrio gigas
Mutation(s): No

Deposited: 2002-06-19 Released: 2003-02-20
Deposition Author(s): Raaijmakers, H.C.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.201 (Depositor)
R-Value Work:
0.167 (Depositor)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.4 of the entry. See complete history.

Literature

Gene Sequence and the 1.8 A Crystal Structure of the Tungsten-Containing Formate Dehydrogenase from Desulfovibrio Gigas

Raaijmakers, H.C.A., Macieira, S., Dias, J., Teixeira, S., Bursakov, S., Huber, R., Moura, J., Moura, I., Romao, M.

(2002) Structure 10: 1261

PubMed: 12220497 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00826-2
Primary Citation Related Structures:
1H0H

PubMed Abstract:
Desulfovibrio gigas formate dehydrogenase is the first representative of a tungsten-containing enzyme from a mesophile that has been structurally characterized. It is a heterodimer of 110 and 24 kDa subunits. The large subunit, homologous to E. coli FDH-H and to D. desulfuricans nitrate reductase, harbors the W site and one [4Fe-4S] center. No small subunit ortholog containing three [4Fe-4S] clusters has been reported. The structural homology with E. coli FDH-H shows that the essential residues (SeCys158, His159, and Arg407) at the active site are conserved. The active site is accessible via a positively charged tunnel, while product release may be facilitated, for H(+) by buried waters and protonable amino acids and for CO(2) through a hydrophobic channel.

Organizational Affiliation

REQUIMTE/CQFB, Departamento de Química, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.

Macromolecule Content

Total Structure Weight: 274.27 kDa
Atom Count: 21,055
Modeled Residue Count: 2,382
Deposited Residue Count: 2,382
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMATE DEHYDROGENASE SUBUNIT ALPHA	A, C [auth K]	977	Megalodesulfovibrio gigas	Mutation(s): 0 EC: 1.2.1.2 (PDB Primary Data), 1.17.1.9 (UniProt)
UniProt
Find proteins for Q934F5 (Megalodesulfovibrio gigas) Explore Q934F5 Go to UniProtKB: Q934F5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q934F5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMATE DEHYDROGENASE SUBUNIT BETA	B, D [auth L]	214	Megalodesulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for Q8GC87 (Megalodesulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759)) Explore Q8GC87 Go to UniProtKB: Q8GC87
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8GC87
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2MD Query on 2MD Download:Ideal Coordinates CCD File SDF format, chain P [auth K] SDF format, chain F [auth A] MOL2 format, chain P [auth K] MOL2 format, chain F [auth A] mmCIF format, chain P [auth K] mmCIF format, chain F [auth A]	F [auth A], P [auth K]	GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER C₂₀ H₂₈ N₁₀ O₁₃ P₂ S₂ YDYCAANTTOPADF-JKOCJXFLSA-N		Interactions Focus chain F [auth A] Focus chain P [auth K]
MGD Query on MGD Download:Ideal Coordinates CCD File SDF format, chain Q [auth K] SDF format, chain G [auth A] MOL2 format, chain Q [auth K] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth K] mmCIF format, chain G [auth A]	G [auth A], Q [auth K]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth K]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain W [auth L] SDF format, chain V [auth L] SDF format, chain S [auth K] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain X [auth L] MOL2 format, chain W [auth L] MOL2 format, chain V [auth L] MOL2 format, chain S [auth K] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain X [auth L] mmCIF format, chain W [auth L] mmCIF format, chain V [auth L] mmCIF format, chain S [auth K] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A] L [auth B] M [auth B] N [auth B] S [auth K] I [auth A], L [auth B], M [auth B], N [auth B], S [auth K], V [auth L], W [auth L], X [auth L]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth K] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain U [auth K] SDF format, chain K [auth A] MOL2 format, chain U [auth K] MOL2 format, chain K [auth A] mmCIF format, chain U [auth K] mmCIF format, chain K [auth A]	K [auth A], U [auth K]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain U [auth K]
W Query on W Download:Ideal Coordinates CCD File SDF format, chain O [auth K] SDF format, chain E [auth A] MOL2 format, chain O [auth K] MOL2 format, chain E [auth A] mmCIF format, chain O [auth K] mmCIF format, chain E [auth A]	E [auth A], O [auth K]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth K]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain T [auth K] SDF format, chain J [auth A] MOL2 format, chain T [auth K] MOL2 format, chain J [auth A] mmCIF format, chain T [auth K] mmCIF format, chain J [auth A]	J [auth A], T [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain T [auth K]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain R [auth K] SDF format, chain H [auth A] MOL2 format, chain R [auth K] MOL2 format, chain H [auth A] mmCIF format, chain R [auth K] mmCIF format, chain H [auth A]	H [auth A], R [auth K]	UNKNOWN ATOM OR ION X		Interactions Focus chain H [auth A] Focus chain R [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.201 (Depositor)
R-Value Work: 0.167 (Depositor)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.408	α = 90
b = 110.398	β = 93.53
c = 156.185	γ = 90

Software Package:

Software Name	Purpose
O	model building
SCALEPACK	data scaling
SHARP	phasing
AMoRE	phasing
ARP/wARP	phasing
O	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-02-20

Deposition Author(s):

Raaijmakers, H.C.A.

Revision History (Full details and data files)

Version 1.0: 2003-02-20
Type: Initial release
Version 1.1: 2014-01-29
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2017-06-28
Changes: Refinement description
Version 2.0: 2019-01-23
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2019-04-03
Changes: Data collection, Experimental preparation
Version 2.2: 2019-05-08
Changes: Data collection, Experimental preparation
Version 2.3: 2023-12-13
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
Version 2.4: 2024-10-23
Changes: Structure summary