3UOE

The crystal structure of dehydrogenase from Sinorhizobium meliloti

PDB DOI: https://doi.org/10.2210/pdb3UOE/pdb

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

Deposited: 2011-11-16 Released: 2011-11-30
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: 2.31 Å
R-Value Free:
0.245 (Depositor), 0.236 (DCC)
R-Value Work:
0.189 (Depositor), 0.184 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of dehydrogenase from Sinorhizobium meliloti

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

To be published.

Macromolecule Content

Total Structure Weight: 76.03 kDa
Atom Count: 5,069
Modelled Residue Count: 658
Deposited Residue Count: 714
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrogenase	A, B	357	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: RA0141, SMa0265
UniProt
Find proteins for Q930Q4 (Rhizobium meliloti (strain 1021)) Explore Q930Q4 Go to UniProtKB: Q930Q4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q930Q4
Sequence Annotations Expand
Reference Sequence LOADING

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: 2.31 Å
R-Value Free: 0.245 (Depositor), 0.236 (DCC)
R-Value Work: 0.189 (Depositor), 0.184 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.708	α = 90
b = 79.692	β = 90
c = 107.129	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-30

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-11-30
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary