1KO0

Crystal Structure of a D,L-lysine complex of diaminopimelate decarboxylase

• PDB DOI: https://doi.org/10.2210/pdb1KO0/pdb

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


• Deposited: 2001-12-19 Released: 2003-11-11 
• Deposition Author(s): Levdikov, V., Blagova, L., Bose, N., Momany, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.181 

Starting Model: experimental

Literature

Diaminopimelate Decarboxylase uses a Versatile Active Site for Stereospecific Decarboxylation

Levdikov, V., Blagova, L., Bose, N., Momany, C.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 47.46 kDa 
• Atom Count: 3,693 
• Modelled Residue Count: 419 
• Deposited Residue Count: 425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A	425	Escherichia coli	Mutation(s): 0  Gene Names: lysA EC: 4.1.1.20
UniProt
Find proteins for P00861 (Escherichia coli (strain K12)) Explore P00861  Go to UniProtKB:  P00861

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
DLY	D [auth A]	D-LYSINE C6 H14 N2 O2 KDXKERNSBIXSRK-RXMQYKEDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.181 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.997	α = 90
b = 98.997	β = 90
c = 176.966	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-11 
Deposition Author(s): Levdikov, V., Blagova, L., Bose, N., Momany, C.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description