4FSH | pdb_00004fsh

Crystal Structure of Shikimate Dehydrogenase (aroE) Clinical Variant v2356 from Helicobacter pylori in Complex with Shikimate

PDB DOI: https://doi.org/10.2210/pdb4FSH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-06-27 Released: 2013-01-30
Deposition Author(s): Cheng, W.C., Chen, T.J., Wang, W.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.260 (Depositor), 0.220 (DCC)
R-Value Work:
0.214 (Depositor), 0.210 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Shikimate Dehydrogenase (aroE) Clinical Variant v2356 from Helicobacter pylori in Complex with Shikimate

Cheng, W.C., Chen, T.J., Wang, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 60.85 kDa
Atom Count: 4,150
Modeled Residue Count: 523
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate dehydrogenase	A, B	271	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: aroE, HP_1249 EC: 1.1.1.25
UniProt
Find proteins for P56119 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56119 Go to UniProtKB: P56119
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56119
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SKM Query on SKM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C₇ H₁₀ O₅ JXOHGGNKMLTUBP-HSUXUTPPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.260 (Depositor), 0.220 (DCC)
R-Value Work: 0.214 (Depositor), 0.210 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.118	α = 90
b = 71.87	β = 90
c = 176.388	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-30
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, 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.