3NA8 | pdb_00003na8

Crystal Structure of a putative dihydrodipicolinate synthetase from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb3NA8/pdb

• Classification: LYASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-01 Released: 2011-06-01 
• Deposition Author(s): Qiu, W., Lam, R., Romanov, V., Jones, K., Pai, E.F., Chirgadze, N.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.270 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Crystal Structure of a putative dihydrodipicolinate synthetase from Pseudomonas aeruginosa

Qiu, W., Lam, R., Romanov, V., Jones, K., Pai, E.F., Chirgadze, N.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 137.87 kDa 
• Atom Count: 9,849 
• Modeled Residue Count: 1,162 
• Deposited Residue Count: 1,260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative dihydrodipicolinate synthetase	A, B, C, D	315	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA0223 EC: 4.2.1.52
UniProt
Find proteins for Q9I6R5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I6R5  Go to UniProtKB:  Q9I6R5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT	F [auth A], I [auth C], K [auth D]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
MG	E [auth A], G [auth B], H [auth C], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.270 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.37	α = 90
b = 156.21	β = 90
c = 76.58	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHARP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Qiu, W., Lam, R., Romanov, V., Jones, K., Pai, E.F., Chirgadze, N.Y.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-15
  Changes: Non-polymer description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary