3PUL | pdb_00003pul

Crystal structure of the complex of Dhydrodipicolinate synthase from Acinetobacter baumannii with lysine at 2.3A resolution

• PDB DOI: https://doi.org/10.2210/pdb3PUL/pdb

• Classification: LYASE
• Organism(s): Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-06 Released: 2010-12-29 
• Deposition Author(s): Jithesh, O., Yamini, S., Kaur, N., Gautam, A., Tewari, R., Kushwaha, G.S., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.228 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of Dhydrodipicolinate synthase from Acinetobacter baumannii with lysine at 2.3A resolution

Jithesh, O., Yamini, S., Kaur, N., Gautam, A., Tewari, R., Kushwaha, G.S., Kaur, P., Srinivasan, A., Sharma, S., 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: 63.42 kDa 
• Atom Count: 4,752 
• Modeled Residue Count: 582 
• Deposited Residue Count: 582 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	291	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0  Gene Names: DHDPS, HMPREF0010_03414 EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for D0CFC3 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0CFC3  Go to UniProtKB:  D0CFC3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	F [auth B]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.228 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.813	α = 90
b = 168.813	β = 90
c = 62.678	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Jithesh, O., Yamini, S., Kaur, N., Gautam, A., Tewari, R., Kushwaha, G.S., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-12-29
  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