4FOS | pdb_00004fos

Crystal Structure of Shikimate Dehydrogenase (aroE) Q237A Mutant from Helicobacter pylori in Complex with Shikimate

• PDB DOI: https://doi.org/10.2210/pdb4FOS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-06-21 Released: 2012-12-26 
• Deposition Author(s): Cheng, W.C., Chen, T.J., Wang, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.5 kDa 
• Atom Count: 2,186 
• Modelled Residue Count: 263 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate dehydrogenase	A	271	Helicobacter pylori 26695	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SKM	B [auth A]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C7 H10 O5 JXOHGGNKMLTUBP-HSUXUTPPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.311	α = 90
b = 62.718	β = 90
c = 84.03	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Cheng, W.C., Chen, T.J., Wang, W.C.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description