3V2H | pdb_00003v2h

The crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti

PDB DOI: https://doi.org/10.2210/pdb3V2H/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-12-12 Released: 2011-12-28
Deposition Author(s): Zhang, Z., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.286 (Depositor), 0.280 (DCC)
R-Value Work:
0.226 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti

Zhang, Z., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 60.83 kDa
Atom Count: 3,417
Modeled Residue Count: 463
Deposited Residue Count: 562
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-beta-hydroxybutyrate dehydrogenase	A, B	281	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: bdhA, RB1136, SMb21010 EC: 1.1.1.30
UniProt
Find proteins for O86034 (Rhizobium meliloti (strain 1021)) Explore O86034 Go to UniProtKB: O86034
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O86034
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 3.00 Å
R-Value Free: 0.286 (Depositor), 0.280 (DCC)
R-Value Work: 0.226 (Depositor), 0.230 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.166	α = 90
b = 89.166	β = 90
c = 140.318	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-12-28

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-12-28
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-10-09
Changes: Structure summary