3C5Q

Crystal structure of diaminopimelate decarboxylase (I148L mutant) from Helicobacter pylori complexed with L-lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori

Hu, T.Wu, D.Ding, J.Jiang, H.Shen, X.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diaminopimelate decarboxylase425Helicobacter pyloriMutation(s): 0 
Gene Names: lysA
EC: 4.1.1.20
UniProt
Find proteins for B4XMC6 (Helicobacter pylori)
Explore B4XMC6 
Go to UniProtKB:  B4XMC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4XMC6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.111α = 90
b = 79.111β = 90
c = 134.821γ = 120
Software Package:
Software NamePurpose
d*TREKdata processing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations