4DGS | pdb_00004dgs

The crystals structure of dehydrogenase from Rhizobium meliloti

PDB DOI: https://doi.org/10.2210/pdb4DGS/pdb

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

Deposited: 2012-01-26 Released: 2012-02-08
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: 2.50 Å
R-Value Free:
0.284 (Depositor), 0.292 (DCC)
R-Value Work:
0.255 (Depositor)
R-Value Observed:
0.257 (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 crystals structure of dehydrogenase from Rhizobium meliloti

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

To be published.

Macromolecule Content

Total Structure Weight: 36.84 kDa
Atom Count: 2,113
Modeled Residue Count: 277
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrogenase	A	340	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: RA0043, SMa0085
UniProt
Find proteins for Q931A1 (Rhizobium meliloti (strain 1021)) Explore Q931A1 Go to UniProtKB: Q931A1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q931A1
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.284 (Depositor), 0.292 (DCC)
R-Value Work: 0.255 (Depositor)
R-Value Observed: 0.257 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.657	α = 90
b = 71.155	β = 96.39
c = 55.148	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: 2012-02-08

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-02-08
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: 2024-11-27
Changes: Structure summary