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) 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PQS (software)

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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

Entry History 

Deposition Data

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

Revision History  

• 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