1ZOB | pdb_00001zob

Crystal structure of dialkylglycine decarboxylases bound with calcium ion

• PDB DOI: https://doi.org/10.2210/pdb1ZOB/pdb

• Classification: LYASE
• Organism(s): Burkholderia cepacia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-05-12 Released: 2006-08-08 
• Deposition Author(s): Liu, W., Toney, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.277 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.221 (DCC) 

Starting Model: experimental

Literature

Crystal structures of dialkylglycine decarboxylase bound with cesium ion and calcium ion

Liu, W., Toney, M.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 47.08 kDa 
• Atom Count: 3,345 
• Modeled Residue Count: 431 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,2-dialkylglycine decarboxylase	A	433	Burkholderia cepacia	Mutation(s): 0  EC: 4.1.1.64
UniProt
Find proteins for P16932 (Burkholderia cepacia) Explore P16932  Go to UniProtKB:  P16932

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	D [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MES	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.277 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.221 (DCC) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.553	α = 90
b = 150.553	β = 90
c = 84.703	γ = 120

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
CNS	refinement
PROTEUM PLUS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Liu, W., Toney, M.D.

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description