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- PDB-5cyv: Crystal structure of CouR from Rhodococcus jostii RHA1 bound to p... -

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Basic information

Entry
Database: PDB / ID: 5cyv
TitleCrystal structure of CouR from Rhodococcus jostii RHA1 bound to p-coumaroyl-CoA
ComponentsTranscriptional regulator
KeywordsTranscriptional regulator / TRANSCRIPTION REGULATOR / p-hydroxycinnamate metabolism / MCSG / PF04017 / PSI-BIOLOGY / MARR / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


DNA-binding transcription factor activity / metal ion binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / : / 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 ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / : / 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
ACETATE ION / p-coumaroyl-CoA / Transcriptional regulator
Similarity search - Component
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsStogios, P.J. / Xu, X. / Dong, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: The activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanism.
Authors: Otani, H. / Stogios, P.J. / Xu, X. / Nocek, B. / Li, S.N. / Savchenko, A. / Eltis, L.D.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72411
Polymers31,6582
Non-polymers2,0669
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-82 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.145, 134.385, 73.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-500-

HOH

21B-514-

HOH

31B-537-

HOH

DetailsDimer according to SEC-MALS

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcriptional regulator


Mass: 15828.976 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (strain RHA1) (bacteria)
Strain: RHA1 / Gene: RHA1_ro05125 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0S6D0

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Non-polymers , 5 types, 461 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-WCA / p-coumaroyl-CoA


Mass: 913.677 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C30H42N7O18P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 80 microL of native protein at 21 mg/ml were preincubated with 20 microL of 25 mM p-hydroxycinnamoyl-CoA. Reservoir = 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 4% (w/v) 2- ...Details: 80 microL of native protein at 21 mg/ml were preincubated with 20 microL of 25 mM p-hydroxycinnamoyl-CoA. Reservoir = 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 4% (w/v) 2-methyl-2,4-pentanediol and 26% (w/v) PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2014
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.51→25 Å / Num. obs: 48946 / % possible obs: 97.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 67
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.79 / % possible all: 83.6

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIX1.9_1692refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FM5

3fm5


Resolution: 1.52→24.789 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 3774 4.09 %Random selection
Rwork0.1606 ---
obs0.1623 48184 97.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→24.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 10 452 2706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182344
X-RAY DIFFRACTIONf_angle_d1.853173
X-RAY DIFFRACTIONf_dihedral_angle_d22.358977
X-RAY DIFFRACTIONf_chiral_restr0.084355
X-RAY DIFFRACTIONf_plane_restr0.009411
LS refinement shellResolution: 1.52→1.5393 Å
RfactorNum. reflection% reflection
Rfree0.2747 127 -
Rwork0.2673 2788 -
obs--83 %

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