1UR3 | pdb_00001ur3

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 (Depositor), 0.249 (DCC)
R-Value Work:
0.200 (Depositor), 0.192 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1UR3

This is version 1.3 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
Modeled Residue Count: 298
Deposited Residue Count: 319
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.249 (DCC)
R-Value Work: 0.200 (Depositor), 0.192 (DCC)
R-Value Observed: 0.200 (Depositor)

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

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View more in-depth experimental data

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
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Other, Structure summary

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.