1CC1

CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM

Structural Biology Knowledgebase: 1CC1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 1CC1

Classification: OXIDOREDUCTASE

Total Structure Weight: 87446.20

Macromolecule Entities
Molecule Chains Length Organism Details
HYDROGENASE (SMALL SUBUNIT) S 283 Desulfomicrobium baculatum EC#: 1.12.99.6 IUBMB
Mutation: G99A
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HYDROGENASE (LARGE SUBUNIT) L 498 Desulfomicrobium baculatum EC#: 1.12.7.2 IUBMB
Mutation: V381R
Details: COMPLEXED WITH IRON/SULFUR CLUSTER, CARBONMONOXIDE-(DICYANO) IRON, HYDROSULFURIC ACID
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SF4
Query on SF4

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

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

L NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

L FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
H2S
Query on H2S

L HYDROSULFURIC ACID
HYDROGEN SULFIDE (Synonym)
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
SEC
Query on SEC
L-PEPTIDE LINKING C3 H7 N O2 Se --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.194
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 110.39 α = 90.00
b = 63.70 β = 90.00
c = 99.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-03-03
  • Released Date: 1999-06-01
  • Deposition author(s): Garcin, E., Vernede, X., Hatchikian, E.C., Volbeda, A., Frey, M., Fontecilla-Camps, J.C.

Revision History

  • 2014-08-06
    Type: Polymer description | Details: Introduce one letter code for SEC
  • 2014-08-06
    Type: Linkage | Details: Remove polymer links to SEC
  • 2014-02-19
    Type: Atom nomenclature | Details: Change CSE to SEC
  • 2014-02-19
    Type: Polymer description | Details: Change CSE to SEC
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4