3WSE | pdb_00003wse

Reduced HcgD from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb3WSE/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-13 Released: 2014-08-27 
• Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.221 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis

Fujishiro, T., Ermler, U., Shima, S.

(2014) FEBS Lett 588: 2789-2793

• PubMed: 24931373 
• DOI: https://doi.org/10.1016/j.febslet.2014.05.059
• Primary Citation Related Structures: 
  3WSD, 3WSE, 3WSF, 3WSG, 3WSH, 3WSI


• PubMed Abstract: 
  

  HcgD, a homolog of the ubiquitous Nif3-like protein family, is found in a gene cluster involved in the biosynthesis of the iron-guanylylpyridinol (FeGP) cofactor of [Fe]-hydrogenase. The presented crystal structure and biochemical analyses indicated that HcgD has a dinuclear iron-center, which provides a pronounced binding site for anionic ligands. HcgD contains a stronger and a weaker bound iron; the latter being removable by chelating reagents preferentially in the oxidized state. Therefore, we propose HcgD as an iron chaperone in FeGP cofactor biosynthesis, which might also stimulate investigations on the functionally unknown but physiologically important eukaryotic Nif3-like protein family members.

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Organizational Affiliation: 
• Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.
Max Planck Institute for Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt/Main, Germany.
Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany; PRESTO, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 170.77 kDa 
• Atom Count: 11,973 
• Modeled Residue Count: 1,473 
• Deposited Residue Count: 1,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative GTP cyclohydrolase 1 type 2	A, B, C, D, E, F	252	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: MJ0927

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE2	G [auth A], H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], S [auth E], T [auth E], V [auth F], W [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.221 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.01	α = 90
b = 134.98	β = 90
c = 161.62	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
EPMR	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description