3WB2

HcgB from Methanocaldococcus jannaschii in complex with the guanylyl-pyridinol product in a model reaction of [Fe]-hydrogenase cofactor biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb3WB2/pdb

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


• Deposited: 2013-05-11 Released: 2014-02-05 
• Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.226 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Starting Model: experimental

Literature

Identification of the HcgB enzyme in [Fe]-hydrogenase-cofactor biosynthesis.

Fujishiro, T., Tamura, H., Schick, M., Kahnt, J., Xie, X., Ermler, U., Shima, S.

(2013) Angew Chem Int Ed Engl 52: 12555-12558

• PubMed: 24249552 
• DOI: https://doi.org/10.1002/anie.201306745
• Primary Citation of Related Structures:  
  3WB0, 3WB1, 3WB2

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Organizational Affiliation: 

Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse 10, 35043 Marburg (Germany) http://www.mpi-marburg.mpg.de/

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 77.91 kDa 
• Atom Count: 5,284 
• Modelled Residue Count: 634 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MJ0488	A, B, C, D	166	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: HcgB, MJ0488
UniProt
Find proteins for Q57912 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57912  Go to UniProtKB:  Q57912

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YGP	E [auth A], F [auth A], J [auth C], K [auth C]	5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine C17 H21 N6 O9 P SHYVQHDJQQBUQP-UBEDBUPSSA-N
GDP	H [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	G [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.226 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.01	α = 90
b = 97.37	β = 90
c = 63.54	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description