5L10 | pdb_00005l10

Crystal Structure of N-Acylhomoserine Lactone Dependent LuxR Family Transcriptionl Factor CepR2 from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb5L10/pdb

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

Deposited: 2016-07-28 Released: 2016-10-26
Deposition Author(s): Kim, Y., Chhor, G., Jedrzejczak, R., Winan, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.217 (Depositor), 0.216 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of N-Acylhomoserine Lactone Dependent LuxR Family Transcriptionl Factor CepR2 from Burkholderia cenocepacia.

Kim, Y., Chhor, G., Jedrzejczak, R., Winan, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 117.09 kDa
Atom Count: 8,072
Modeled Residue Count: 1,002
Deposited Residue Count: 1,038
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acylhomoserine lactone dependent regulatory protein	A, B, C, D, E A, B, C, D, E, F	173	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAM0188
UniProt
Find proteins for B4EHM0 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EHM0 Go to UniProtKB: B4EHM0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4EHM0
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 Q [auth E] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A] I [auth A] J [auth B] L [auth C] N [auth D] G [auth A], I [auth A], J [auth B], L [auth C], N [auth D], O [auth D], Q [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain S [auth F] MOL2 format, chain S [auth F] mmCIF format, chain S [auth F]	S [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain S [auth F] Interactions & Density Focus chain S [auth F]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B], M [auth C], P [auth D], R [auth E]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth E] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain R [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.217 (Depositor), 0.216 (DCC)
R-Value Work: 0.182 (Depositor), 0.183 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.276	α = 90
b = 74.594	β = 117.29
c = 118.027	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Structure summary