2V8Z

Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12

• PDB DOI: https://doi.org/10.2210/pdb2V8Z/pdb

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


• Deposited: 2007-08-16 Released: 2008-03-04 
• Deposition Author(s): Manicka, S., Peleg, Y., Unger, T., Albeck, S., Dym, O., Greenblatt, H.M., Bourenkov, G., Lamzin, V., Krishnaswamy, S., Sussman, J.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.232 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Crystal Structure of Yage, a Putative Dhdps Like Protein from Escherichia Coli K12.

Manicka, S., Peleg, Y., Unger, T., Albeck, S., Dym, O., Greenblatt, H.M., Bourenkov, G., Lamzin, V., Krishnaswamy, S., Sussman, J.L.

(2008) Proteins 71: 2102

• PubMed: 18361457 
• DOI: https://doi.org/10.1002/prot.22023
• Primary Citation of Related Structures:  
  2V8Z, 2V9D, 4PTN

---

Organizational Affiliation: 

School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamilnadu, India.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.05 kDa 
• Atom Count: 9,478 
• Modelled Residue Count: 1,192 
• Deposited Residue Count: 1,372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YAGE	A, B, C, D	343	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P75682 (Escherichia coli (strain K12)) Explore P75682  Go to UniProtKB:  P75682

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.232 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.689	α = 90
b = 156.494	β = 90
c = 55.884	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Manicka, S., Peleg, Y., Unger, T., Albeck, S., Dym, O., Greenblatt, H.M., Bourenkov, G., Lamzin, V., Krishnaswamy, S., Sussman, J.L.

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description