3ZE9

3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the oxidized as-isolated state at 1.33 Angstroms

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 2.0 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT
A
283Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: hysB
EC: 1.12.7.2
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  Q72AS4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING
B
484Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: hysA
EC: 1.12.7.2
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  Q72AS3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FCO
Query on FCO
Download SDF File 
Download CCD File 
B
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FSX
Query on FSX
Download SDF File 
Download CCD File 
A
BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)
FE4-S3-O3 CLUSTER
Fe4 O3 S3
BIOGFUMNBIDAOG-VNBKSMEUCR
 Ligand Interaction
FE2
Query on FE2
Download SDF File 
Download CCD File 
B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI
Download SDF File 
Download CCD File 
B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
PSW
Query on PSW
B
L-PEPTIDE LINKINGC3 H7 N O2 S SeSEC
CSS
Query on CSS
A
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
OCS
Query on OCS
B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.131 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.694α = 90.00
b = 63.348β = 105.42
c = 109.740γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description
  • Version 1.2: 2014-05-14
    Type: Atomic model
  • Version 1.3: 2014-11-05
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 1.4: 2018-06-27
    Type: Advisory, Data collection, Derived calculations
  • Version 2.0: 2019-04-24
    Type: Atomic model, Data collection, Experimental preparation, Polymer sequence