3OQP | pdb_00003oqp

Crystal structure of a putative isochorismatase (Bxe_A0706) from BURKHOLDERIA XENOVORANS LB400 at 1.22 A resolution

PDB DOI: https://doi.org/10.2210/pdb3OQP/pdb

Classification: HYDROLASE
Organism(s): Paraburkholderia xenovorans LB400
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-03 Released: 2010-10-13
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free:
0.166 (Depositor), 0.173 (DCC)
R-Value Work:
0.140 (Depositor), 0.150 (DCC)
R-Value Observed:
0.141 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3OQP

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a putative isochorismatase (Bxe_A0706) from BURKHOLDERIA XENOVORANS LB400 at 1.22 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 45.56 kDa
Atom Count: 3,829
Modeled Residue Count: 416
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative isochorismatase	A, B	211	Paraburkholderia xenovorans LB400	Mutation(s): 0 Gene Names: Bxeno_A3690, Bxe_A0706
UniProt
Find proteins for Q13UL1 (Paraburkholderia xenovorans (strain LB400)) Explore Q13UL1 Go to UniProtKB: Q13UL1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13UL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.22 Å
R-Value Free: 0.166 (Depositor), 0.173 (DCC)
R-Value Work: 0.140 (Depositor), 0.150 (DCC)
R-Value Observed: 0.141 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.369	α = 90
b = 103.135	β = 98.94
c = 45.062	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2014-11-12
Changes: Non-polymer description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2023-02-01
Changes: Database references, Derived calculations
Version 1.6: 2024-10-30
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.