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- PDB-1z9c: Crystal structure of OhrR bound to the ohrA promoter: Structure o... -

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Basic information

Entry
Database: PDB / ID: 1z9c
TitleCrystal structure of OhrR bound to the ohrA promoter: Structure of MarR family protein with operator DNA
Components
  • (DNA (29-MER)) x 2
  • Organic hydroperoxide resistance transcriptional regulator
KeywordsTRANSCRIPTION/DNA / OhrR / MarR family protein / bacterial transcription factor / Winged HTH protein / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


response to stress / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to hydrogen peroxide / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
Transcriptional regulator SarA/Rot / : / 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 SarA/Rot / : / 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) / Organic hydroperoxide resistance transcriptional regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsHong, M. / Fuangthong, M. / Helmann, J.D. / Brennan, R.G.
CitationJournal: Mol.Cell / Year: 2005
Title: Structure of an OhrR-ohrA Operator Complex Reveals the DNA Binding Mechanism of the MarR Family.
Authors: Hong, M. / Fuangthong, M. / Helmann, J.D. / Brennan, R.G.
History
DepositionApr 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: DNA (29-MER)
H: DNA (29-MER)
I: DNA (29-MER)
J: DNA (29-MER)
K: DNA (29-MER)
L: DNA (29-MER)
A: Organic hydroperoxide resistance transcriptional regulator
B: Organic hydroperoxide resistance transcriptional regulator
C: Organic hydroperoxide resistance transcriptional regulator
D: Organic hydroperoxide resistance transcriptional regulator
E: Organic hydroperoxide resistance transcriptional regulator
F: Organic hydroperoxide resistance transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)155,48712
Polymers155,48712
Non-polymers00
Water3,135174
1
G: DNA (29-MER)
H: DNA (29-MER)
A: Organic hydroperoxide resistance transcriptional regulator
B: Organic hydroperoxide resistance transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)51,8294
Polymers51,8294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: DNA (29-MER)
J: DNA (29-MER)
C: Organic hydroperoxide resistance transcriptional regulator
D: Organic hydroperoxide resistance transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)51,8294
Polymers51,8294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: DNA (29-MER)
L: DNA (29-MER)
E: Organic hydroperoxide resistance transcriptional regulator
F: Organic hydroperoxide resistance transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)51,8294
Polymers51,8294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.899, 80.960, 109.340
Angle α, β, γ (deg.)90.00, 100.20, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological dimer was observed in the structure of OhrR-DNA complex

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Components

#1: DNA chain DNA (29-MER)


Mass: 8895.792 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: DNA chain DNA (29-MER)


Mass: 8913.820 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Protein
Organic hydroperoxide resistance transcriptional regulator


Mass: 17009.727 Da / Num. of mol.: 6 / Mutation: C15S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ohrR / Plasmid: pET16x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: O34777
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.7
Details: pH 3.7, 0.1 M MgCl2 and 5 to 8 % of PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2PEG 800011
3MgCl212
4PEG 800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2004
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.64→59.65 Å / Num. all: 47153 / Num. obs: 47153 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 11.1
Reflection shellResolution: 2.64→2.76 Å / % possible obs: 98.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / Num. measured obs: 6956 / Rsym value: 0.386 / % possible all: 96.9

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Phasing

Phasing MRRfactor: 0.528 / Cor.coef. Fo:Fc: 0.36
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
EPMR2.5phasing
CNS1.1refinement
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→59.65 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1281466.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2012 5 %RANDOM
Rwork0.216 ---
all0.216 39953 --
obs0.216 39953 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.594 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1--8.15 Å20 Å2-0.07 Å2
2---1.81 Å20 Å2
3---9.96 Å2
Refinement stepCycle: LAST / Resolution: 2.64→59.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6413 3486 0 174 10073
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.20
X-RAY DIFFRACTIONc_dihedral_angle_d19.60
X-RAY DIFFRACTIONc_improper_angle_d1.540
X-RAY DIFFRACTIONc_mcbond_it0
X-RAY DIFFRACTIONc_mcangle_it0
X-RAY DIFFRACTIONc_scbond_it0
X-RAY DIFFRACTIONc_scangle_it0
LS refinement shellResolution: 2.64→2.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 317 4.7 %
Rwork0.318 6447 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2dna-rna.topdna-rna_rep.param
X-RAY DIFFRACTION3water.topwater_rep.param
X-RAY DIFFRACTION4ion.topion.param

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