4GIC

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)

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)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q606Q2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

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