4G9I

Crystal structure of T.kodakarensis HypF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.279 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1.

Tominaga, T.Watanabe, S.Matsumi, R.Atomi, H.Imanaka, T.Miki, K.

(2012) Acta Crystallogr.,Sect.F 68: 1153-1157

  • DOI: 10.1107/S1744309112036421

  • PubMed Abstract: 
  • HypF is involved in the biosynthesis of the CN ligand of the NiFe(CN)(2)CO centre of [NiFe]-hydrogenases. Here, the full-length structure of HypF from Thermococcus kodakarenesis is reported at 4.5 Å resolution. The N-terminal acylphosphatase-like (AC ...

    HypF is involved in the biosynthesis of the CN ligand of the NiFe(CN)(2)CO centre of [NiFe]-hydrogenases. Here, the full-length structure of HypF from Thermococcus kodakarenesis is reported at 4.5 Å resolution. The N-terminal acylphosphatase-like (ACP) domain interacts with the zinc-finger domain with some flexibility in its relative position. Molecular-surface analysis shows that a deep pocket formed between the ACP and zinc-finger domains is highly conserved and has positive potential. These results suggest that the positively charged pocket identified is involved in the hydrolysis of carbamoyl phosphate and the formation of a carbamoyl intermediate.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase maturation protein HypF
A, B, C, D, E, F
772Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)Mutation(s): 0 
EC: 6.2.-.-
Find proteins for Q5JII4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Go to UniProtKB:  Q5JII4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.279 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 265.810α = 90.00
b = 265.810β = 90.00
c = 693.712γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release