3USE

Crystal Structure of E. coli hydrogenase-1 in its as-isolated form

Structural Biology Knowledgebase: 3USE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.120

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3USE

Classification: OXIDOREDUCTASE

Total Structure Weight: 208046.84

Macromolecule Entities
Molecule Chains Length Organism Details
Hydrogenase-1 small chain S, T 335 Escherichia coli EC#: 1.12.99.6 IUBMB
Gene Name(s): hyaA b0972 JW0954
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Hydrogenase-1 large chain L, M 582 Escherichia coli EC#: 1.12.99.6 IUBMB
Gene Name(s): hyaB b0973 JW0955
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Oxidoreductases

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


Small Molecules
Ligands 12 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LMT
Query on LMT

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

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

S, T FE4-S3 CLUSTER
T-CLUSTER (Synonym)
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF3
Query on SF3

S, T FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-DXQBTJNKAZ
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F3S
Query on F3S

S, T FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FCO
Query on FCO

L, M CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

M, S, T SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

L GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3NI
Query on 3NI

L, M NICKEL (III) ION
Ni
JDRCAGKFDGHRNQ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

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

L, M MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LI
Query on LI

L, M LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.120
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.93 α = 90.00
b = 97.79 β = 90.00
c = 183.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-11-23
  • Released Date: 2012-03-28
  • Deposition author(s): Volbeda, A., Fontecilla-Camps, J.C., Darnault, C.

Revision History

  • 2012-04-18
    Type: Citation | Details: Citation update