3TDF

Crystal structure of the complex of Dihydrodipicolinate synthase from Acinetobacter baumannii with 2-Ketobutanoic acid at 1.99 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3TDF/pdb

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


• Deposited: 2011-08-11 Released: 2011-08-31 
• Deposition Author(s): Kumar, M., Kaushik, S., Sinha, M., Kaur, P., Tewari, R., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.220 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Crystal structure of the complex of Dihydrodipicolinate synthase from Acinetobacter baumannii with 2-Ketobutanoic acid at 1.99 A resolution

Kumar, M., Kaushik, S., Sinha, M., Kaur, P., Tewari, R., 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: 62.76 kDa 
• Atom Count: 4,909 
• Modelled 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
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2KT	C [auth A], D [auth B]	2-KETOBUTYRIC ACID C4 H6 O3 TYEYBOSBBBHJIV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.220 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.235	α = 90
b = 121.947	β = 115.9
c = 51.131	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Kumar, M., Kaushik, S., Sinha, M., Kaur, P., Tewari, R., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection