3PHJ | pdb_00003phj

Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with 3-Dehydroshikimate

• PDB DOI: https://doi.org/10.2210/pdb3PHJ/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., Lin, C.H., Wang, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with 3-Dehydroshikimate

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

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.63 kDa 
• Atom Count: 4,156 
• Modeled Residue Count: 510 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate dehydrogenase	A, B	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHK	C [auth A], D [auth B]	3-DEHYDROSHIKIMATE C7 H10 O5 YVYKOQWMJZXRRM-UYFOZJQFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.593	α = 90
b = 47.156	β = 97.63
c = 124.124	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

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Cheng, W.C., Lin, S.C., Lin, C.H., Wang, W.C.

Revision History  

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