4OHC | pdb_00004ohc

Crystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb4OHC/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-01-17 Released: 2014-02-05
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.197 (Depositor), 0.205 (DCC)
R-Value Work:
0.156 (Depositor), 0.167 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia cenocepacia

Lukacs, C.M., Abendroth, J., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 160.25 kDa
Atom Count: 11,660
Modeled Residue Count: 1,332
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotate phosphoribosyltransferase	A, B, C, D, E A, B, C, D, E, F	236	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: pyrE, BCAL0204 EC: 2.4.2.10
UniProt
Find proteins for B4E589 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4E589 Go to UniProtKB: B4E589
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4E589
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F]	G [auth A] H [auth A] K [auth B] N [auth C] P [auth D] G [auth A], H [auth A], K [auth B], N [auth C], P [auth D], S [auth E], V [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E]	I [auth A] J [auth A] L [auth B] O [auth C] Q [auth D] I [auth A], J [auth A], L [auth B], O [auth C], Q [auth D], T [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain T [auth E] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain T [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] mmCIF format, chain M [auth B] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F]	M [auth B], R [auth D], U [auth E], W [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain M [auth B] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.197 (Depositor), 0.205 (DCC)
R-Value Work: 0.156 (Depositor), 0.167 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.31	α = 105.83
b = 82.97	β = 104.27
c = 83.1	γ = 117.36

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-02-05

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-02-05
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description