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- PDB-6c9t: Transcriptional repressor, CouR -

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Basic information

Entry
Database: PDB / ID: 6c9t
TitleTranscriptional repressor, CouR
ComponentsCouR
KeywordsDNA BINDING PROTEIN / Transcriptional regulation / repressor / MarR family
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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
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 1.3Oct 4, 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

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Assembly

Deposited unit
A: CouR
B: CouR


Theoretical massNumber of molelcules
Total (without water)40,5072
Polymers40,5072
Non-polymers00
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-52 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.008, 59.008, 108.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein CouR / Transcriptional regulator / MarR family


Mass: 20253.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Gene: RPA1794 / Plasmid: pET28-MBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6N8V9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% Tacsimate (v/v) pH 7.0

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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: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.073→59.01 Å / Num. obs: 22136 / % possible obs: 98.3 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.024 / Rrim(I) all: 0.07 / Net I/σ(I): 21
Reflection shellResolution: 2.073→2.108 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.946 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.85 / Rpim(I) all: 0.343 / Rrim(I) all: 1.007 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C2S

6c2s


Resolution: 2.07→59.01 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.867 / SU B: 9.625 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33441 1057 4.8 %RANDOM
Rwork0.27184 ---
obs0.27508 21079 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.007 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å2-0 Å2-0 Å2
2--1.12 Å2-0 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 2.07→59.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 0 316 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192115
X-RAY DIFFRACTIONr_bond_other_d0.0020.022145
X-RAY DIFFRACTIONr_angle_refined_deg1.7072.0042848
X-RAY DIFFRACTIONr_angle_other_deg1.04634919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32222.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2215400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9351527
X-RAY DIFFRACTIONr_chiral_restr0.0840.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022298
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02433
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_it3.5494.5841072
X-RAY DIFFRACTIONr_mcbond_other3.5434.5841071
X-RAY DIFFRACTIONr_mcangle_it5.0426.8561333
X-RAY DIFFRACTIONr_mcangle_other5.046.8561334
X-RAY DIFFRACTIONr_scbond_it3.0344.7551043
X-RAY DIFFRACTIONr_scbond_other3.0334.7541044
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3657.0591516
X-RAY DIFFRACTIONr_long_range_B_refined7.7856.4892565
X-RAY DIFFRACTIONr_long_range_B_other7.63256.0312480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.073→2.126 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 75 -
Rwork0.371 1575 -
obs--100 %

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