3VAB | pdb_00003vab

Crystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP

• PDB DOI: https://doi.org/10.2210/pdb3VAB/pdb

• Classification: LYASE
• Organism(s): Brucella melitensis bv. 1 str. 16M
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-29 Released: 2012-01-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP

Edwards, T.E., Gardberg, A.S., Letesson, J.J., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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: 96.73 kDa 
• Atom Count: 7,198 
• Modeled Residue Count: 840 
• Deposited Residue Count: 886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase 1	A, B	443	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0  Gene Names: BMEI0084, lysA1 EC: 4.1.1.20
UniProt
Find proteins for Q8YJJ9 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YJJ9  Go to UniProtKB:  Q8YJJ9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33VAB

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.53	α = 90
b = 126.37	β = 112.71
c = 68.18	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection