3CNV

Crystal structure of the ligand-binding domain of a putative GntR-family transcriptional regulator from Bordetella bronchiseptica

PDB DOI: https://doi.org/10.2210/pdb3CNV/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Bordetella bronchiseptica RB50
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-03-26 Released: 2008-04-29
Deposition Author(s): Zimmerman, M.D., Xu, X., Cui, H., Filippova, E.V., Savchenko, A., Edwards, A.M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.217 (Depositor), 0.060 (DCC)
R-Value Work:
0.164 (Depositor), 0.310 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the ligand-binding domain of a putative GntR-family transcriptional regulator from Bordetella bronchiseptica.

Zimmerman, M.D., Xu, X., Cui, H., Filippova, E.V., Savchenko, A., Edwards, A.M., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 75.46 kDa
Atom Count: 5,485
Modelled Residue Count: 634
Deposited Residue Count: 648
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 GntR-family transcriptional regulator	A, B, C, D	162	Bordetella bronchiseptica RB50	Mutation(s): 0 Gene Names: BB3683
UniProt
Find proteins for A0A0H3LYW6 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LYW6 Go to UniProtKB: A0A0H3LYW6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3LYW6
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], H [auth B], I [auth B], K [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.217 (Depositor), 0.060 (DCC)
R-Value Work: 0.164 (Depositor), 0.310 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.196	α = 82.36
b = 58.071	β = 86.52
c = 65.58	γ = 68.31

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-2000	data reduction
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-2000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-04-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2011-10-05
Changes: Structure summary
Version 1.3: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Structure summary