5WRF

Crystal structure of dodecameric type II dehydroquinate dehydratase from Acinetobacter baumannii with unexplained connecting electron density between free cysteine residues of molecular pairs

PDB DOI: https://doi.org/10.2210/pdb5WRF/pdb

Classification: LYASE
Organism(s): Acinetobacter baumannii ATCC 17978
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-01 Released: 2016-12-21
Deposition Author(s): Iqbal, N., Singh, P.K., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.256
R-Value Work: 0.209
R-Value Observed: 0.210

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of dodecameric type II dehydroquinate dehydratase from Acinetobacter baumannii with unexplained connecting electron density between free cysteine residues of molecular pairs

Iqbal, N., Singh, P.K., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 190.58 kDa
Atom Count: 13,645
Modelled Residue Count: 1,740
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	145	Acinetobacter baumannii ATCC 17978	Mutation(s): 0 Gene Names: aroQ, A1S_2009 EC: 4.2.1.10
UniProt
Find proteins for A3M692 (Acinetobacter baumannii (strain ATCC 17978 / DSM 105126 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377)) Explore A3M692 Go to UniProtKB: A3M692
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3M692
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.256
R-Value Work: 0.209
R-Value Observed: 0.210
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.801	α = 90
b = 135.75	β = 97.53
c = 142.74	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-21
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.