2QGH

Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori complexed with L-lysine

• PDB DOI: https://doi.org/10.2210/pdb2QGH/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-06-28 Released: 2008-05-27 
• Deposition Author(s): Hu, T., Wu, D., Jiang, H., Shen, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.206 

Starting Model: experimental

Literature

Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori complexed with L-lysine

Hu, T., Wu, D., Jiang, H., Shen, X.

To be published.

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: 47.96 kDa 
• Atom Count: 3,254 
• Modelled Residue Count: 394 
• Deposited Residue Count: 425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A	425	Helicobacter pylori	Mutation(s): 0  Gene Names: lysA EC: 4.1.1.20
UniProt
Find proteins for B4XMC6 (Helicobacter pylori) Explore B4XMC6  Go to UniProtKB:  B4XMC6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
LYS	C [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.206 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.248	α = 90
b = 79.248	β = 90
c = 134.275	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Hu, T., Wu, D., Jiang, H., Shen, X.

Revision History  

• 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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description