1QY9

Crystal structure of E. coli Se-MET protein YDDE

• PDB DOI: https://doi.org/10.2210/pdb1QY9/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.05 Å
• R-Value Free: 0.207 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

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 of 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 130.85 kDa 
• Atom Count: 9,702 
• Modelled Residue Count: 1,183 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL PROTEIN yddE	A, B, C, D	297	Escherichia coli	Mutation(s): 6  Gene Names: YDDE
UniProt
Find proteins for P37757 (Escherichia coli (strain K12)) Explore P37757  Go to UniProtKB:  P37757

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OH	G [auth B]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.207 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.035	α = 90
b = 56.529	β = 101.67
c = 148.742	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

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