4DYV | pdb_00004dyv

Crystal structure of a short-chain dehydrogenase/reductase SDR from Xanthobacter autotrophicus Py2

PDB DOI: https://doi.org/10.2210/pdb4DYV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Xanthobacter versatilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-02-29 Released: 2012-03-14
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Hillerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Gizzi, A., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.205 (Depositor), 0.202 (DCC)
R-Value Work:
0.166 (Depositor), 0.168 (DCC)
R-Value Observed:
0.168 (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/reductase SDR from Xanthobacter autotrophicus Py2

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

To be published.

Macromolecule Content

Total Structure Weight: 29.14 kDa
Atom Count: 1,751
Modeled Residue Count: 213
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A	272	Xanthobacter versatilis	Mutation(s): 0 Gene Names: Xaut_2039
UniProt
Find proteins for A7IGZ0 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)) Explore A7IGZ0 Go to UniProtKB: A7IGZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7IGZ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.80 Å
R-Value Free: 0.205 (Depositor), 0.202 (DCC)
R-Value Work: 0.166 (Depositor), 0.168 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.901	α = 90
b = 83.046	β = 90
c = 93.503	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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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary