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- PDB-6pco: Mechanism for regulation of DNA binding of Bordetella bronchisept... -

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Basic information

Entry
Database: PDB / ID: 6pco
TitleMechanism for regulation of DNA binding of Bordetella bronchiseptica BpsR by 6-hydroxynicotinic acid
ComponentsMarR-family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Inhibition / Biofilm / Transcription Regulation / Bordetella / BpsR
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity
Similarity search - Function
: / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,4-BUTANEDIOL / MarR-family transcriptional regulator
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBooth, W.T. / Davis, R.R. / Deora, R. / Hollis, T.
CitationJournal: Plos One / Year: 2019
Title: Structural mechanism for regulation of DNA binding of BpsR, a Bordetella regulator of biofilm formation, by 6-hydroxynicotinic acid.
Authors: Booth, W.T. / Davis, R.R. / Deora, R. / Hollis, T.
History
DepositionJun 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MarR-family transcriptional regulator
B: MarR-family transcriptional regulator
C: MarR-family transcriptional regulator
D: MarR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9615
Polymers86,8714
Non-polymers901
Water18010
1
A: MarR-family transcriptional regulator
B: MarR-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5253
Polymers43,4352
Non-polymers901
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-33 kcal/mol
Surface area13490 Å2
MethodPISA
2
C: MarR-family transcriptional regulator
D: MarR-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,4352
Polymers43,4352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-27 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.870, 90.523, 103.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MarR-family transcriptional regulator


Mass: 21717.639 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB1771 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0H3LTT0
#2: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.25 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 2250, 0.2 M potassium formate, and 15% butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 8, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.65→34.03 Å / Num. obs: 17964 / % possible obs: 98.65 % / Redundancy: 1.1 % / Biso Wilson estimate: 70.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.034 / Rrim(I) all: 0.068 / Net I/σ(I): 23.4
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 4.38 / Num. unique obs: 1712 / CC1/2: 0.906 / Rpim(I) all: 0.33 / Rrim(I) all: 0.642 / % possible all: 97.44

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-3000717.1data reduction
HKL-3000717.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NNN

2nnn


Resolution: 2.75→34.03 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / SU B: 13.702 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.794 / ESU R Free: 0.395 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30139 895 5.1 %RANDOM
Rwork0.23116 ---
obs0.23479 16513 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.499 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å20 Å2
2---0.08 Å20 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 2.75→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 6 10 3528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0143567
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173273
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.6544850
X-RAY DIFFRACTIONr_angle_other_deg0.911.6337605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81220.608181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68615568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4311533
X-RAY DIFFRACTIONr_chiral_restr0.060.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5427.4941866
X-RAY DIFFRACTIONr_mcbond_other5.5367.4921865
X-RAY DIFFRACTIONr_mcangle_it8.02711.212322
X-RAY DIFFRACTIONr_mcangle_other8.02511.2142323
X-RAY DIFFRACTIONr_scbond_it6.3457.8781701
X-RAY DIFFRACTIONr_scbond_other6.3237.8781701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.25711.6382529
X-RAY DIFFRACTIONr_long_range_B_refined11.13189.7243957
X-RAY DIFFRACTIONr_long_range_B_other11.13289.7323958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 53 -
Rwork0.338 1207 -
obs--97.37 %

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