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.

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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, dapA, HTZ92_3489 EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2KT Query on 2KT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	2-KETOBUTYRIC ACID C₄ H₆ O₃ TYEYBOSBBBHJIV-UHFFFAOYSA-N		Ligand Interaction

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.