3NOE | pdb_00003noe

Crystal Structure of Dihydrodipicolinate synthase from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb3NOE/pdb

• Classification: LYASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-06-25 Released: 2010-07-28 
• Deposition Author(s): Kaur, N., Kumar, S., Singh, N., Gautam, A., Sharma, R., Sharma, S., Tewari, R., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.234 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Dihydrodipicolinate synthase from Pseudomonas aeruginosa

Kaur, N., Kumar, S., Singh, N., Gautam, A., Sharma, R., Sharma, S., Tewari, R., Singh, T.P.

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: 63.46 kDa 
• Atom Count: 4,608 
• Modeled Residue Count: 584 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	292	Pseudomonas aeruginosa PAO1	Mutation(s): 4  EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for Q9I4W3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4W3  Go to UniProtKB:  Q9I4W3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.234 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.42	α = 90
b = 81.87	β = 90
c = 124.8	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Kaur, N., Kumar, S., Singh, N., Gautam, A., Sharma, R., Sharma, S., Tewari, R., Singh, T.P.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description