4X00 | pdb_00004x00

X-ray crystal structure of a putative aryl esterase from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb4X00/pdb

Classification: HYDROLASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-20 Released: 2014-12-03
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.166 (Depositor), 0.166 (DCC)
R-Value Work:
0.137 (Depositor), 0.137 (DCC)
R-Value Observed:
0.138 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

X-ray crystal structure of a putative aryl esterase from Burkholderia cenocepacia

Fairman, J.W., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 125.84 kDa
Atom Count: 9,851
Modeled Residue Count: 1,090
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydrolase	A, B, C, D	283	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL2527
UniProt
Find proteins for B4E794 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4E794 Go to UniProtKB: B4E794
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4E794
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain L [auth A] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain L [auth A] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain L [auth A]	L [auth A], S [auth C], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain L [auth A] Focus chain S [auth C] Focus chain W [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], U [auth D], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D]
F Query on F Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain P [auth B] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain P [auth B] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain P [auth B]	P [auth B], T [auth C], X [auth D]	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M		Interactions Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.166 (Depositor), 0.166 (DCC)
R-Value Work: 0.137 (Depositor), 0.137 (DCC)
R-Value Observed: 0.138 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.72	α = 90
b = 80.37	β = 93.07
c = 99.4	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2015-02-04
Changes: Derived calculations
Version 1.2: 2017-09-06
Changes: Author supporting evidence, Derived calculations, Source and taxonomy
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 1.4: 2024-02-28
Changes: Data collection, Database references