3TCE

Crystal structure of the complex of Dihydrodipicolinate synthase from Acinetobacter baumannii with 5-Hydroxylysine at 2.6 A resolution

PDB DOI: https://doi.org/10.2210/pdb3TCE/pdb

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

Deposited: 2011-08-09 Released: 2011-08-31
Deposition Author(s): Shukla, P.K., Kaushik, S., Sinha, M., Kaur, P., Tewari, R., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.264
R-Value Work: 0.233
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the complex of Dihydrodipicolinate synthase from Acinetobacter baumannii with 5-Hydroxylysine at 2.6 A resolution

Shukla, P.K., Kaushik, S., Sinha, M., Kaur, P., Tewari, R., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 62.88 kDa
Atom Count: 4,750
Modelled Residue Count: 582
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

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(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
LYZ Query on LYZ 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]	5-HYDROXYLYSINE C₆ H₁₄ N₂ O₃ YSMODUONRAFBET-UHNVWZDZSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.264
R-Value Work: 0.233
R-Value Observed: 0.233
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.602	α = 90
b = 121.721	β = 114.39
c = 50.125	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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.