1UR3

Crystal structure of the apo form of the E.coli ydhF protein

PDB DOI: https://doi.org/10.2210/pdb1UR3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2003-10-24 Released: 2003-12-04
Deposition Author(s): Jeudy, S., Claverie, J.M., Abergel, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.256
R-Value Work: 0.200
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Ydhf the E.Coli Aldo-Keto Reductase Ydhf

Jeudy, S., Claverie, J.M., Abergel, C.

To be published.

Macromolecule Content

Total Structure Weight: 36.67 kDa
Atom Count: 2,438
Modelled Residue Count: 298
Deposited Residue Count: 319
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL OXIDOREDUCTASE YDHF	A [auth M]	319	Escherichia coli K-12	Mutation(s): 0 EC: 1
UniProt
Find proteins for P76187 (Escherichia coli (strain K12)) Explore P76187 Go to UniProtKB: P76187
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P76187
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth M] MOL2 format, chain B [auth M]	B [auth M]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth M] Interactions & Density Focus chain B [auth M]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.256
R-Value Work: 0.200
R-Value Observed: 0.200
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.722	α = 90
b = 87.722	β = 90
c = 66.168	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-12-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-12-04
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.