6SDV

W-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Towards the mechanistic understanding of enzymatic CO2 reduction

Oliveira, A.R.Mota, C.Mourato, C.Domingos, R.M.Santos, M.F.A.Gesto, D.Guigliarelli, B.Santos-Silva, T.Romao, M.J.Pereira, I.C.

(2020) ACS Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit1,009Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
EC: 1.2.1.2
UniProt
Find proteins for Q72EJ1 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72EJ1 
Go to UniProtKB:  Q72EJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72EJ1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, beta subunit, putative236Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
UniProt
Find proteins for Q72EJ0 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72EJ0 
Go to UniProtKB:  Q72EJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72EJ0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD (Subject of Investigation/LOI)
Query on MGD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
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

Download Ideal Coordinates CCD File 
E [auth A],
U [auth B],
V [auth B],
W [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
W (Subject of Investigation/LOI)
Query on W

Download Ideal Coordinates CCD File 
F [auth A]TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
T [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
R [auth A],
S [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)
Query on H2S

Download Ideal Coordinates CCD File 
G [auth A]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.885α = 90
b = 128.56β = 90
c = 149.629γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BBB-EBB/2723/2014
Fundacao para a Ciencia e a TecnologiaPortugalUID/Multi/04378/2019

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary