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- PDB-6c2s: Transcriptional repressor, CouR, bound to a 23-mer DNA duplex -

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Basic information

Entry
Database: PDB / ID: 6c2s
TitleTranscriptional repressor, CouR, bound to a 23-mer DNA duplex
Components
  • (23-mer) x 2
  • Transcriptional regulator, MarR familyTranscriptional regulation
KeywordsDNA BINDING PROTEIN/DNA / Transcriptional regulation / repressor / MarR family / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis of transcriptional regulation by CouR, a repressor of coumarate catabolism, inRhodopseudomonas palustris.
Authors: Cogan, D.P. / Baraquet, C. / Harwood, C.S. / Nair, S.K.
History
DepositionJan 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Transcriptional regulator, MarR family
U: 23-mer
B: Transcriptional regulator, MarR family
V: 23-mer
C: Transcriptional regulator, MarR family
X: 23-mer
D: Transcriptional regulator, MarR family
Y: 23-mer


Theoretical massNumber of molelcules
Total (without water)109,2428
Polymers109,2428
Non-polymers00
Water48627
1
A: Transcriptional regulator, MarR family
U: 23-mer
V: 23-mer
D: Transcriptional regulator, MarR family


Theoretical massNumber of molelcules
Total (without water)54,6214
Polymers54,6214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-70 kcal/mol
Surface area19880 Å2
MethodPISA
2
B: Transcriptional regulator, MarR family
C: Transcriptional regulator, MarR family
X: 23-mer
Y: 23-mer


Theoretical massNumber of molelcules
Total (without water)54,6214
Polymers54,6214
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-75 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.580, 58.750, 168.090
Angle α, β, γ (deg.)90.00, 105.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Transcriptional regulator, MarR family / Transcriptional regulation / CouR


Mass: 20253.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1794 / Plasmid: pET28-MBP / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Rosetta / References: UniProt: Q6N8V9
#2: DNA chain 23-mer


Mass: 7003.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rhodopseudomonas palustris (phototrophic)
#3: DNA chain 23-mer


Mass: 7110.659 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rhodopseudomonas palustris (phototrophic)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.1 M ammonium phosphate, 12% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 30186 / % possible obs: 99.6 % / Redundancy: 4.74 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.34
Reflection shellResolution: 2.85→2.95 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→32.738 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 1497 5 %
Rwork0.2154 --
obs0.218 29930 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→32.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 1874 0 27 6293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116552
X-RAY DIFFRACTIONf_angle_d1.559238
X-RAY DIFFRACTIONf_dihedral_angle_d19.0423692
X-RAY DIFFRACTIONf_chiral_restr0.0711092
X-RAY DIFFRACTIONf_plane_restr0.009864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9420.41231370.35522599X-RAY DIFFRACTION100
2.942-3.0470.42741340.33282540X-RAY DIFFRACTION100
3.047-3.16890.37651310.32422524X-RAY DIFFRACTION97
3.1689-3.3130.3661330.27172520X-RAY DIFFRACTION97
3.313-3.48750.32511320.26492507X-RAY DIFFRACTION96
3.4875-3.70570.3081380.25562608X-RAY DIFFRACTION100
3.7057-3.99140.27441350.21932576X-RAY DIFFRACTION100
3.9914-4.39220.2581380.19452613X-RAY DIFFRACTION100
4.3922-5.02580.23261380.1812622X-RAY DIFFRACTION100
5.0258-6.32450.24191390.19312637X-RAY DIFFRACTION100
6.3245-32.73990.1751420.14732687X-RAY DIFFRACTION98

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