3PHH | pdb_00003phh

Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate

PDB DOI: https://doi.org/10.2210/pdb3PHH/pdb

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

Deposited: 2010-11-04 Released: 2011-11-09
Deposition Author(s): Cheng, W.C., Lin, S.C., Wang, W.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.227 (Depositor), 0.225 (DCC)
R-Value Work:
0.197 (Depositor), 0.196 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3PHH

Ligand Structure Quality Assessment

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

Literature

Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate

Cheng, W.C., Lin, S.C., Wang, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 30.31 kDa
Atom Count: 2,425
Modeled Residue Count: 260
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate dehydrogenase	A	269	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C₇ H₁₀ O₅ JXOHGGNKMLTUBP-HSUXUTPPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.227 (Depositor), 0.225 (DCC)
R-Value Work: 0.197 (Depositor), 0.196 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.37	α = 90
b = 62.798	β = 90
c = 84.38	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.