6CNZ | pdb_00006cnz

Crystal Structure of Chorismate Mutase from Burkholderia thailandensis

PDB DOI: https://doi.org/10.2210/pdb6CNZ/pdb
Entry: 6CNZ supersedes: 4OJ7

Classification: ISOMERASE
Organism(s): Burkholderia thailandensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-03-09 Released: 2018-03-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.216 (Depositor), 0.218 (DCC)
R-Value Work:
0.164 (Depositor), 0.167 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of chorismate mutase from Burkholderia thailandensis.

Asojo, O.A., Dranow, D.M., Serbzhinskiy, D., Subramanian, S., Staker, B., Edwards, T.E., Myler, P.J.

(2018) Acta Crystallogr F Struct Biol Commun 74: 294-299

PubMed: 29717997 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X1800506X
Primary Citation Related Structures:
6CNZ

PubMed Abstract:
Burkholderia thailandensis is often used as a model for more virulent members of this genus of proteobacteria that are highly antibiotic-resistant and are potential agents of biological warfare that are infective by inhalation. As part of ongoing efforts to identify potential targets for the development of rational therapeutics, the structures of enzymes that are absent in humans, including that of chorismate mutase from B. thailandensis, have been determined by the Seattle Structural Genomics Center for Infectious Disease. The high-resolution structure of chorismate mutase from B. thailandensis was determined in the monoclinic space group P2 ₁ with three homodimers per asymmetric unit. The overall structure of each protomer has the prototypical AroQγ topology and shares conserved binding-cavity residues with other chorismate mutases, including those with which it has no appreciable sequence identity.

Organizational Affiliation

National School of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue Suite 550, Mail Stop BCM320, Houston, TX 77030-3411, USA.

Macromolecule Content

Total Structure Weight: 117.78 kDa
Atom Count: 7,800
Modeled Residue Count: 964
Deposited Residue Count: 1,080
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate mutase	A, B, C, D, E A, B, C, D, E, F	180	Burkholderia thailandensis	Mutation(s): 0 Gene Names: AQ477_14105, CRX59_12655 EC: 5.4.99.5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain BA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain BA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain BA [auth E]	BA [auth E] M [auth B] N [auth B] O [auth B] S [auth C] BA [auth E], M [auth B], N [auth B], O [auth B], S [auth C], T [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Z [auth D]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain DA [auth F] SDF format, chain CA [auth E] SDF format, chain AA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] CA [auth E] DA [auth F] EA [auth F] FA [auth F] AA [auth E], CA [auth E], DA [auth F], EA [auth F], FA [auth F], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], P [auth C], Q [auth C], R [auth C], U [auth C], V [auth C], W [auth D], X [auth D], Y [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.216 (Depositor), 0.218 (DCC)
R-Value Work: 0.164 (Depositor), 0.167 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.71	α = 90
b = 121.38	β = 99.99
c = 88.67	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

This entry supersedes: 4OJ7

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2018-05-09
Changes: Data collection, Database references
Version 1.2: 2018-05-16
Changes: Data collection, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-10-09
Changes: Structure summary