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- PDB-4o8b: Crystal structure of transcriptional regulator BswR -

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Basic information

Entry
Database: PDB / ID: 4o8b
TitleCrystal structure of transcriptional regulator BswR
ComponentsUncharacterized protein
KeywordsDNA BINDING PROTEIN / HTH motif / transcriptional activator / promoter DNA
Function / homology
Function and homology information


positive regulation of single-species biofilm formation / negative regulation of cell motility / DNA-binding transcription activator activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription
Similarity search - Function
Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYe, F.Z. / Wang, C. / Kumar, V. / Zhang, L.H. / Gao, Y.G.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: BswR controls bacterial motility and biofilm formation in Pseudomonas aeruginosa through modulation of the small RNA rsmZ.
Authors: Wang, C. / Ye, F. / Kumar, V. / Gao, Y.G. / Zhang, L.H.
History
DepositionDec 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,1131
Polymers14,1131
Non-polymers00
Water90150
1
A: Uncharacterized protein

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,2262
Polymers28,2262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2880 Å2
ΔGint-35 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.965, 43.915, 35.019
Angle α, β, γ (deg.)90.00, 115.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein / BswR


Mass: 14113.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2780 / Plasmid: pET26M / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I063
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 20% w/v Polyethylene glycol 10000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 3818 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.085 / Net I/σ(I): 6.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1870 / Rsym value: 0.221 / % possible all: 83.5

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Processing

Software
NameClassification
CrystalCleardata collection
BALBESphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LFP

3lfp


Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.286 207 Random
Rwork0.229 --
obs0.229 3818 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.61 Å20 Å2-3.795 Å2
2---6.466 Å20 Å2
3----8.144 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 0 50 853
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.98
X-RAY DIFFRACTIONc_bond_d0.0045
X-RAY DIFFRACTIONc_mcangle_it1.7
X-RAY DIFFRACTIONc_mcbond_it1.044
X-RAY DIFFRACTIONc_scangle_it2.741
X-RAY DIFFRACTIONc_scbond_it1.779

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