4GIC | pdb_00004gic

Crystal Structure Of a Putative Histidinol dehydrogenase (Target PSI-014034) from Methylococcus capsulatus

• PDB DOI: https://doi.org/10.2210/pdb4GIC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methylococcus capsulatus str. Bath
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-08 Released: 2012-08-22 
• Deposition Author(s): Kumar, P.R., Ahmed, M., Banu, N., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Gizzi, A., Glen, S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Washington, E., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of a putative Histidinol dehydrogenase from Methylococcus capsulatus

Kumar, P.R., Hillerich, B., Love, J., Seidel, R., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 92.01 kDa 
• Atom Count: 6,019 
• Modeled Residue Count: 764 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidinol dehydrogenase	A, B	423	Methylococcus capsulatus str. Bath	Mutation(s): 0  Gene Names: hisD, MCA1963 EC: 1.1.1.23
UniProt
Find proteins for Q606Q2 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore Q606Q2  Go to UniProtKB:  Q606Q2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.04	α = 90
b = 81.517	β = 90
c = 147.036	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Kumar, P.R., Ahmed, M., Banu, N., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Gizzi, A., Glen, S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Washington, E., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary