1H0H

Tungsten containing Formate Dehydrogenase from Desulfovibrio Gigas

Experimental Data Snapshot

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

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

  • DOI: https://doi.org/10.1016/s0969-2126(02)00826-2

  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FORMATE DEHYDROGENASE SUBUNIT ALPHAA,
C [auth K]		977Megalodesulfovibrio gigasMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ934F5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FORMATE DEHYDROGENASE SUBUNIT BETAB,
D [auth L]		214Megalodesulfovibrio gigasMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GC87
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2MD
Query on 2MD
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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
MGD
Query on MGD
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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
SF4
Query on SF4
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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
EPE
Query on EPE
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K [auth A],
U [auth K]		4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
W
Query on W
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E [auth A],
O [auth K]		TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
CA
Query on CA
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J [auth A],
T [auth K]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNX
Query on UNX
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H [auth A],
R [auth K]		UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.408α = 90
b = 110.398β = 93.53
c = 156.185γ = 90
Software Package:
Software NamePurpose
Omodel building
SCALEPACKdata scaling
SHARPphasing
AMoREphasing
ARP/wARPphasing
Ophasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

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