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- PDB-6c28: Transcriptional repressor, CouR, bound to p-coumaroyl-CoA -

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Basic information

Entry
Database: PDB / ID: 6c28
TitleTranscriptional repressor, CouR, bound to p-coumaroyl-CoA
ComponentsTranscriptional regulator, MarR family
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
p-coumaroyl-CoA / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 7, 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
B: Transcriptional regulator, MarR family
C: Transcriptional regulator, MarR family
D: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6698
Polymers81,0144
Non-polymers3,6554
Water4,234235
1
C: Transcriptional regulator, MarR family
hetero molecules

B: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3344
Polymers40,5072
Non-polymers1,8272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_955-x+9/2,-y,z+1/21
2
B: Transcriptional regulator, MarR family
hetero molecules

C: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3344
Polymers40,5072
Non-polymers1,8272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_954-x+9/2,-y,z-1/21
3
A: Transcriptional regulator, MarR family
D: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3344
Polymers40,5072
Non-polymers1,8272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-51 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.854, 104.006, 128.801
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
Transcriptional regulator, MarR family


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: couR, RPA1794 / Plasmid: pET28-MBP / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Rosetta / References: UniProt: Q6N8V9
#2: Chemical
ChemComp-WCA / p-coumaroyl-CoA


Mass: 913.677 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H42N7O18P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.26 Å3/Da / Density % sol: 45.58 % / Description: thick rods
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 M lithium sulfate, 23.5% PEG 4K, 1 mM DTT, 0.085 M Tris-HCl pH 8.5, 15% glycerol

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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: 2.09→128.801 Å / Num. obs: 43271 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Net I/σ(I): 20.5
Reflection shellResolution: 2.09→2.126 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2130 / CC1/2: 0.8 / Rpim(I) all: 0.392 / Rrim(I) all: 1.029 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→80.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.086 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26406 2095 4.8 %RANDOM
Rwork0.20897 ---
obs0.21173 41175 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.386 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20 Å2
2---0.47 Å20 Å2
3----2.71 Å2
Refinement stepCycle: 1 / Resolution: 2.09→80.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 236 235 4703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194724
X-RAY DIFFRACTIONr_bond_other_d0.0020.024604
X-RAY DIFFRACTIONr_angle_refined_deg2.122.0576410
X-RAY DIFFRACTIONr_angle_other_deg1.161310564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8135572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06721.935186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99515823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4121557
X-RAY DIFFRACTIONr_chiral_restr0.1290.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025073
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02960
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_it4.1874.7262294
X-RAY DIFFRACTIONr_mcbond_other4.1794.7252293
X-RAY DIFFRACTIONr_mcangle_it6.0417.0642864
X-RAY DIFFRACTIONr_mcangle_other6.047.0642865
X-RAY DIFFRACTIONr_scbond_it5.435.2772430
X-RAY DIFFRACTIONr_scbond_other5.4295.2762431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0897.7863547
X-RAY DIFFRACTIONr_long_range_B_refined10.04557.0165249
X-RAY DIFFRACTIONr_long_range_B_other10.03256.945218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 150 -
Rwork0.303 2983 -
obs--98.37 %

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