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 

wwPDB Validation 3D Report Full Report


This is version 2.2 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: 10.1016/s0969-2126(02)00826-2
  • Structures With Same Primary Citation

  • 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 ...

    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.


    Related Citations: 
    • Tungsten-Containing Formate Dehydrogenase from Desulfovibrio Gigas: Metal Identification and Preliminary Structural Data by Multi-Wavelength Crystallography
      Raaijmakers, H., Teixeira, S., Dias, J.M., Almendra, M.J., Brondino, C.D., Moura, I., Moura, J., Romao, M.J.
      (2001) J Biol Inorg Chem 6: 398

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FORMATE DEHYDROGENASE SUBUNIT ALPHA
A, K
977Desulfovibrio gigasMutation(s): 0 
Gene Names: fdhA
EC: 1.2.1.2 (PDB Primary Data), 1.17.1.9 (UniProt)
Find proteins for Q934F5 (Desulfovibrio gigas)
Go to UniProtKB:  Q934F5

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FORMATE DEHYDROGENASE SUBUNIT BETA
B, L
214Desulfovibrio gigasMutation(s): 0 
Find proteins for Q8GC87 (Desulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759))
Go to UniProtKB:  Q8GC87
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2MD
Query on 2MD

Download CCD File 
A, 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
 Ligand Interaction
MGD
Query on MGD

Download CCD File 
A, 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
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
A, B, K, L
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
EPE
Query on EPE

Download CCD File 
A, K
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
W
Query on W

Download CCD File 
A, K
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, K
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A, K
UNKNOWN ATOM OR ION
X
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

  • 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