6AL9 | pdb_00006al9

Crystal structure of chorismate mutase from Helicobacter pylori in complex with prephenate

• PDB DOI: https://doi.org/10.2210/pdb6AL9/pdb

• Classification: ISOMERASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-07 Released: 2018-11-07 
• Deposition Author(s): Fan, Y., Jameson, G.B., Panjikar, S., Parker, E.J.
• Funding Organization(s): Marsden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of chorismate mutase from Helicobacter pylori in complex with prephenate

Fan, Y., Jameson, G.B., Panjikar, S., Parker, E.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, gel filtration, homology

Macromolecule Content 

• Total Structure Weight: 23.15 kDa 
• Atom Count: 1,533 
• Modeled Residue Count: 181 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate mutase	A, B	96	Helicobacter pylori	Mutation(s): 0  Gene Names: HP_0291 EC: 5.4.99.5
UniProt
Find proteins for O25064 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25064  Go to UniProtKB:  O25064

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRE	C [auth A]	PREPHENIC ACID C10 H10 O6 FPWMCUPFBRFMLH-XGAOUMNUSA-N
PHB	E [auth B]	P-HYDROXYBENZOIC ACID C7 H6 O3 FJKROLUGYXJWQN-UHFFFAOYSA-N
PYR	D [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.869	α = 90
b = 63.526	β = 90
c = 166.918	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Fan, Y., Jameson, G.B., Panjikar, S., Parker, E.J.

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Funding Organization	Location	Grant Number
Marsden	New Zealand	UOC1105

Revision History  

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection