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

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Basic information

Entry
Database: PDB / ID: 6pcp
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


DNA-binding transcription factor activity
Similarity search - Function
Winged helix DNA-binding domain / MarR-type HTH domain profile. / 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
6-hydroxypyridine-3-carboxylic acid / MarR family transcriptional regulator
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 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
E: MarR family transcriptional regulator
F: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,19912
Polymers106,3646
Non-polymers8356
Water1448
1
A: MarR family transcriptional regulator
D: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7334
Polymers35,4552
Non-polymers2782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-31 kcal/mol
Surface area13410 Å2
MethodPISA
2
B: MarR family transcriptional regulator
C: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7334
Polymers35,4552
Non-polymers2782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-34 kcal/mol
Surface area13480 Å2
MethodPISA
3
E: MarR family transcriptional regulator
F: MarR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7334
Polymers35,4552
Non-polymers2782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-31 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.543, 110.571, 273.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
MarR family transcriptional regulator


Mass: 17727.361 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: marR_2, ERS014547_01166 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0T7MD48
#2: Chemical
ChemComp-OA7 / 6-hydroxypyridine-3-carboxylic acid / 6-hydroxynicotinic acid


Mass: 139.109 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 2 mM 6-HNA, 0.2 M MgCl2, 18.5 % PEG 3350

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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: DECTRIS PILATUS3 R 100K-A / Detector: PIXEL / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→30.086 Å / Num. obs: 18178 / % possible obs: 90.78 % / Redundancy: 6.4 % / Biso Wilson estimate: 45.62 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.049 / Rrim(I) all: 0.134 / Net I/σ(I): 15.18
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 5.71 / Num. unique obs: 1564 / CC1/2: 0.966 / Rpim(I) all: 0.097 / Rrim(I) all: 0.21 / % possible all: 79.39

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000717.1data reduction
HKL-3000717.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PCO

6pco


Resolution: 3.2→30.086 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 0 / Phase error: 25.72
RfactorNum. reflection% reflection
Rfree0.269 1805 10.01 %
Rwork0.2165 --
obs0.2221 18028 90.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→30.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6089 0 60 8 6157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036250
X-RAY DIFFRACTIONf_angle_d0.6628531
X-RAY DIFFRACTIONf_dihedral_angle_d9.0413742
X-RAY DIFFRACTIONf_chiral_restr0.041055
X-RAY DIFFRACTIONf_plane_restr0.0041105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.28640.33681180.27411051X-RAY DIFFRACTION79
3.2864-3.3830.34291250.28291122X-RAY DIFFRACTION82
3.383-3.4920.33421200.24771097X-RAY DIFFRACTION82
3.492-3.61670.32761280.251141X-RAY DIFFRACTION85
3.6167-3.76120.32081320.26571171X-RAY DIFFRACTION86
3.7612-3.9320.32691280.22631165X-RAY DIFFRACTION86
3.932-4.13880.30571390.20871239X-RAY DIFFRACTION91
4.1388-4.39740.23531450.20141286X-RAY DIFFRACTION95
4.3974-4.73570.23631490.18381351X-RAY DIFFRACTION98
4.7357-5.21010.22631550.19121384X-RAY DIFFRACTION99
5.2101-5.95890.28221500.22521369X-RAY DIFFRACTION100
5.9589-7.48840.25781580.22031406X-RAY DIFFRACTION100
7.4884-30.08760.18331580.17311441X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 43.9618 Å / Origin y: 26.4418 Å / Origin z: -38.6463 Å
111213212223313233
T0.0077 Å20.0432 Å2-0.0887 Å2-0.1684 Å20.0693 Å2---0.1476 Å2
L0.2441 °20.0062 °20.0806 °2-0.1409 °2-0.1265 °2--0.4459 °2
S-0.0386 Å °-0.0614 Å °-0.134 Å °0.0718 Å °-0.1179 Å °0.0512 Å °-0.1101 Å °0.0838 Å °0.026 Å °
Refinement TLS groupSelection details: all

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