4GD3

Structure of E. coli hydrogenase-1 in complex with cytochrome b

Structural Biology Knowledgebase: 4GD3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.200

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GD3

Classification: OXIDOREDUCTASE / ELECTRON TRANSPORT

Total Structure Weight: 470141.78

Macromolecule Entities
Molecule Chains Length Organism Details
Hydrogenase-1 small chain Q, R, S, T 335 Escherichia coli EC#: 1.12.99.6 IUBMB
Mutation: P242C
Gene Name(s): hyaA b0972 JW0954
Hydrogenase-1 large chain J, K, L, M 582 Escherichia coli EC#: 1.12.99.6 IUBMB
Gene Name(s): hyaB b0973 JW0955
Ni/Fe-hydrogenase 1 B-type cytochrome subunit A, B 235 Escherichia coli Gene Name(s): hyaC b0974 JW0956

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Oxidoreductases

Protein Name: O2-tolerant Hydrogenase-1 in complex with cytochrome b


Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMT
Query on LMT

A, B, R, T DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

Q, R, S, T IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F4S
Query on F4S

Q, R, S, T FE4-S3 CLUSTER
T-CLUSTER (Synonym)
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FCO
Query on FCO

J, K, L, M CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

J, K, L, M NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

J, K, L, M, Q, S CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

J, K, L, M MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.200
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 126.00 α = 90.00
b = 165.30 β = 90.00
c = 212.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-31
  • Released Date: 2013-01-02
  • Deposition author(s): Volbeda, A., Fontecilla-Camps, J.C., Darnault, C.

Revision History

  • 2013-01-30
    Type: Citation | Details: Citation update
  • 2013-01-09
    Type: Citation | Details: Citation update