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), 0.170 (DCC)
R-Value Work:
0.140 (Depositor), 0.150 (DCC)
R-Value Observed:
0.141 (Depositor)

wwPDB Validation 3D Report Full Report

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	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), 0.170 (DCC)
R-Value Work: 0.140 (Depositor), 0.150 (DCC)
R-Value Observed: 0.141 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33OQP

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

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 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.