4WJB

X-ray crystal structure of a putative amidohydrolase/peptidase from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb4WJB/pdb

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

Deposited: 2014-09-29 Released: 2014-10-08
Deposition Author(s): Lukacs, C.M., Dranow, D.M., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.213
R-Value Work: 0.173
R-Value Observed: 0.175

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

X-ray crystal structure of a putative amidohydrolase/peptidase from Burkholderia cenocepacia

Lukacs, C.M., Dranow, D.M., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 183.9 kDa
Atom Count: 13,539
Modelled Residue Count: 1,628
Deposited Residue Count: 1,696
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative amidohydrolase/peptidase	A, B, C, D	424	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAM1221 EC: 3.5.1.87
UniProt
Find proteins for B4EHA1 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EHA1 Go to UniProtKB: B4EHA1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EHA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	F [auth A] G [auth A] M [auth B] N [auth B] O [auth B] F [auth A], G [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	E [auth A], L [auth B], T [auth C], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain X [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain W [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C]	H [auth A] I [auth A] J [auth A] K [auth A] R [auth B] H [auth A], I [auth A], J [auth A], K [auth A], R [auth B], S [auth B], W [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.213
R-Value Work: 0.173
R-Value Observed: 0.175
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M34WJB

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.66	α = 90
b = 113.06	β = 95.5
c = 126.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-10-08
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary