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- PDB-5eri: MarR Protein from Peptoclostridium difficile DA00132 -

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Basic information

Entry
Database: PDB / ID: 5eri
TitleMarR Protein from Peptoclostridium difficile DA00132
ComponentsMarR family transcriptional regulator
KeywordsTRANSCRIPTION / Peptoclostridium difficile / MarR / Transcription factor / DNA-binding
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
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
DNA-binding transcriptional repressor MarR
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYuan, H. / Peng, J.W. / Tan, X.S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Fundation of China21472027 China
National Natural Science Fundation of China31270869 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2017
Title: Crystal structure of the multiple antibiotic resistance regulator MarR from Clostridium difficile.
Authors: Peng, J.W. / Yuan, H. / Tan, X.S.
History
DepositionNov 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 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: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)19,5491
Polymers19,5491
Non-polymers00
Water59433
1
A: MarR family transcriptional regulator

A: MarR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)39,0992
Polymers39,0992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6200 Å2
ΔGint-37 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.569, 66.569, 83.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MarR family transcriptional regulator / Regulator of Multiple Antibiotic Resistance / Transcriptional regulator / MarR family / ...Regulator of Multiple Antibiotic Resistance / Transcriptional regulator / MarR family / Uncharacterized HTH-type transcriptional regulator YybA


Mass: 19549.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Gene: yybA / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A031WDA8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 8~10% 2-Propanol, 0.1 M Tris-Cl

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: RIGAKU / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. obs: 8352 / % possible obs: 93.8 % / Redundancy: 20 % / Net I/σ(I): 77
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 15 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 16.87 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LJ9

1lj9


Resolution: 2.3→25.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.833 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25012 394 4.7 %RANDOM
Rwork0.21151 ---
obs0.21332 7915 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.319 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.3→25.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 0 33 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021260
X-RAY DIFFRACTIONr_bond_other_d0.0010.021272
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9811688
X-RAY DIFFRACTIONr_angle_other_deg0.87332942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4425.86258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.83315270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.36156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02262
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_it5.1845.307611
X-RAY DIFFRACTIONr_mcbond_other5.1875.305610
X-RAY DIFFRACTIONr_mcangle_it6.7027.945762
X-RAY DIFFRACTIONr_mcangle_other6.6987.948763
X-RAY DIFFRACTIONr_scbond_it7.7446.414649
X-RAY DIFFRACTIONr_scbond_other7.7396.418650
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.6699.166927
X-RAY DIFFRACTIONr_long_range_B_refined13.38642.3191459
X-RAY DIFFRACTIONr_long_range_B_other13.38542.3151457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.297→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 26 -
Rwork0.28 586 -
obs--96.38 %

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