3ZE8

3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the reduced state at 1.95 Angstroms

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 

Starting Model: experimental
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This is version 3.3 of the entry. See complete history. 


Literature

Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough

Marques, M.C., Coelho, R., Pereira, I.A.C., Matias, P.M.

(2013) Int J Hydrogen Energy 38: 8664


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT283Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
EC: 1.12.7.2 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for Q72AS4 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72AS4 
Go to UniProtKB:  Q72AS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72AS4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING484Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 1 
EC: 1.12.7.2
UniProt
Find proteins for Q72AS3 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72AS3 
Go to UniProtKB:  Q72AS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72AS3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
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C [auth A],
D [auth A],
E [auth A]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
C15
Query on C15
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F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B]		N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE
C17 H38 N O3 S
IZWSFJTYBVKZNK-UHFFFAOYSA-O
FCO
Query on FCO
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I [auth B]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
NI
Query on NI
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J [auth B]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FE2
Query on FE2
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K [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL
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L [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
PSW
Query on PSW
B
L-PEPTIDE LINKINGC3 H7 N O2 S SeSEC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.227α = 90
b = 97.632β = 90
c = 103.348γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 1.2: 2014-11-05
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2019-04-24
    Changes: Data collection, Derived calculations, Experimental preparation, Polymer sequence
  • Version 3.1: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 3.2: 2020-06-03
    Changes: Advisory, Derived calculations, Other
  • Version 3.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description