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- PDB-5h3r: Crystal Structure of mutant MarR C80S from E.coli complexed with ... -

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Basic information

Entry
Database: PDB / ID: 5h3r
TitleCrystal Structure of mutant MarR C80S from E.coli complexed with operator DNA
Components
  • DNA (5'-D(*CP*AP*TP*AP*CP*TP*TP*GP*CP*CP*TP*GP*GP*GP*CP*AP*AP*TP*AP*TP*T)-3')
  • DNA (5'-D(*GP*AP*AP*TP*AP*TP*TP*GP*CP*CP*CP*AP*GP*GP*CP*AP*AP*GP*TP*AP*T)-3')
  • Multiple antibiotic resistance protein MarR
KeywordsTRANSCRIPTION/DNA / MarR family protein / HTH motif / protein-DNA complex / Transcription Factor / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


cellular response to antibiotic / response to heat / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / 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 ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / 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 / DNA (> 10) / Multiple antibiotic resistance protein MarR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsZhu, R. / Lou, H. / Hao, Z.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2017
Title: Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator.
Authors: Zhu, R. / Hao, Z. / Lou, H. / Song, Y. / Zhao, J. / Chen, Y. / Zhu, J. / Chen, P.R.
History
DepositionOct 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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
C: DNA (5'-D(*CP*AP*TP*AP*CP*TP*TP*GP*CP*CP*TP*GP*GP*GP*CP*AP*AP*TP*AP*TP*T)-3')
D: DNA (5'-D(*GP*AP*AP*TP*AP*TP*TP*GP*CP*CP*CP*AP*GP*GP*CP*AP*AP*GP*TP*AP*T)-3')
A: Multiple antibiotic resistance protein MarR
B: Multiple antibiotic resistance protein MarR


Theoretical massNumber of molelcules
Total (without water)45,5914
Polymers45,5914
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11300 Å2
ΔGint-92 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.435, 67.435, 219.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain DNA (5'-D(*CP*AP*TP*AP*CP*TP*TP*GP*CP*CP*TP*GP*GP*GP*CP*AP*AP*TP*AP*TP*T)-3')


Mass: 6413.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*AP*AP*TP*AP*TP*TP*GP*CP*CP*CP*AP*GP*GP*CP*AP*AP*GP*TP*AP*T)-3')


Mass: 6471.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Multiple antibiotic resistance protein MarR


Mass: 16353.234 Da / Num. of mol.: 2 / Mutation: C80S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: marR, cfxB, inaR, soxQ, b1530, JW5248 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27245
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 5000 MME, sodium cacodylate, magnesium chloride, sodium chloride
PH range: 5.6-6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0055 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0055 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. all: 16064 / Num. obs: 16057 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 55.4 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 24.03
Reflection shellResolution: 2.67→2.72 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q5F

3q5f


Resolution: 2.67→33.717 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 1562 9.8 %
Rwork0.1992 --
obs0.2033 15931 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.2 Å2
Refinement stepCycle: LAST / Resolution: 2.67→33.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 855 0 24 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563177
X-RAY DIFFRACTIONf_angle_d0.7114481
X-RAY DIFFRACTIONf_dihedral_angle_d20.831264
X-RAY DIFFRACTIONf_chiral_restr0.0297538
X-RAY DIFFRACTIONf_plane_restr0.0031421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6704-2.76580.40721520.32941411X-RAY DIFFRACTION99.3
2.7658-2.87640.3641620.31691450X-RAY DIFFRACTION100
2.8764-3.00730.35711560.27961435X-RAY DIFFRACTION99.9
3.0073-3.16570.28671480.24381441X-RAY DIFFRACTION99.2
3.1657-3.36390.26781550.2051414X-RAY DIFFRACTION97.6
3.3639-3.62330.24761550.20641424X-RAY DIFFRACTION99.9
3.6233-3.98740.2131590.17671456X-RAY DIFFRACTION100
3.9874-4.56320.2131580.17671438X-RAY DIFFRACTION100
4.5632-5.74460.21781610.17361447X-RAY DIFFRACTION100
5.7446-33.72020.16341560.14131453X-RAY DIFFRACTION99.4

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