1QYA | pdb_00001qya

CRYSTAL STRUCTURE OF E. COLI PROTEIN YDDE

• PDB DOI: https://doi.org/10.2210/pdb1QYA/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-10 Released: 2004-06-08 
• Deposition Author(s): Grassick, A., Sulzenbacher, G., Roig-Zamboni, V., Campanacci, V., Cambillau, C., Bourne, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase

Grassick, A., Sulzenbacher, G., Roig-Zamboni, V., Campanacci, V., Cambillau, C., Bourne, Y.

(2004) Proteins 55: 764-767

• PubMed: 15103639 
• DOI: https://doi.org/10.1002/prot.20025
• Primary Citation Related Structures: 
  1QY9, 1QYA

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Organizational Affiliation: 
• Architecture et Fonction des Macromolécules Biologiques, CNRS UMR6098, Marseille, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 66.81 kDa 
• Atom Count: 4,920 
• Modeled Residue Count: 600 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL PROTEIN yddE	A, B	307	Escherichia coli	Mutation(s): 0  Gene Names: YDDE EC: 5.1
UniProt
Find proteins for P37757 (Escherichia coli (strain K12)) Explore P37757  Go to UniProtKB:  P37757

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.228 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.159	α = 90
b = 79.631	β = 115.26
c = 77.022	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Grassick, A., Sulzenbacher, G., Roig-Zamboni, V., Campanacci, V., Cambillau, C., Bourne, Y.

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-04-03
  Changes: Refinement description