Macromolecule Content

Total Structure Weight: 77.65 kDa
Atom Count: 5480
Modelled Residue Count: 631
Deposited Residue Count: 664
Unique protein chains: 1

3WB0

HcgB from Methanocaldococcus jannaschii in complex with light-decomposed FeGP cofactor of [Fe]-hydrogenase

PDB DOI: 10.2210/pdb3WB0/pdb

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

Deposited: 2013-05-10 Released: 2014-02-05
Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.275
R-Value Work: 0.227
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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 Search on PubMed
DOI: 10.1002/anie.201306745
Primary Citation of Related Structures:
3WB0, 3WB1, 3WB2

Macromolecules

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(by identity cutoff) | 3D Structure

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 EC: 2.7.7
UniProt
Find proteins for Q57912 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57912 Go to UniProtKB: Q57912
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57912
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FEG Query on FEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine C₁₉ H₂₃ N₆ O₁₁ P GTHOTKPHMGEHFD-ACDAHVMNSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.275
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.96	α = 90
b = 119.34	β = 115.14
c = 55.65	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2013-05-10
Released Date: 2014-02-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-05
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.