4DQX | pdb_00004dqx

Crystal structure of a short chain dehydrogenase from Rhizobium etli CFN 42

PDB DOI: https://doi.org/10.2210/pdb4DQX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhizobium etli CFN 42
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-16 Released: 2012-02-29
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Siedel, 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: 2.00 Å
R-Value Free:
0.198 (Depositor), 0.203 (DCC)
R-Value Work:
0.159 (Depositor), 0.168 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a short chain dehydrogenase from Rhizobium etli CFN 42

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 119.88 kDa
Atom Count: 8,052
Modeled Residue Count: 1,006
Deposited Residue Count: 1,108
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable oxidoreductase protein	A, B, C, D	277	Rhizobium etli CFN 42	Mutation(s): 0 Gene Names: RHE_PD00113
UniProt
Find proteins for Q8KL31 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q8KL31 Go to UniProtKB: Q8KL31
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KL31
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.198 (Depositor), 0.203 (DCC)
R-Value Work: 0.159 (Depositor), 0.168 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.245	α = 90
b = 64.595	β = 96.72
c = 113.353	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AutoSol	phasing
Coot	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary