6AL9

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.237
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate mutase	A, B	96	Helicobacter pylori	Mutation(s): 0 Gene Names: HP_0291
UniProt
Find proteins for O25064 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25064 Go to UniProtKB: O25064
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O25064
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRE Query on PRE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PREPHENIC ACID C₁₀ H₁₀ O₆ FPWMCUPFBRFMLH-XGAOUMNUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PHB Query on PHB Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	P-HYDROXYBENZOIC ACID C₇ H₆ O₃ FJKROLUGYXJWQN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.237
R-Value Work: 0.206
R-Value Observed: 0.208
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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-11-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Marsden	New Zealand	UOC1105

Revision History (Full details and data files)

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

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Help and Resources

6AL9

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)