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- PDB-2pfb: Structure of oxidized OhrR from Xanthamonas campestris -

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Basic information

Entry
Database: PDB / ID: 2pfb
TitleStructure of oxidized OhrR from Xanthamonas campestris
ComponentsTranscriptional regulator OhrR
KeywordsTRANSCRIPTION REGULATOR / transcriptional regulator / 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-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
Organic hydroperoxide resistance transcriptional regulator
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsBrennan, R.G. / Newberry, K.J.
Citation
Journal: Mol.Cell / Year: 2007
Title: Structural Mechanism of Organic Hydroperoxide Induction of the Transcription Regulator OhrR.
Authors: Newberry, K.J. / Fuangthong, M. / Panmanee, W. / Mongkolsuk, S. / Brennan, R.G.
#1: Journal: J.Bacteriol. / Year: 2006
Title: Novel organic hydroperoxide-sensing and responding mechanisms for OhrR, a major bacterial sensor and regulator of organic hydroperoxide stress
Authors: Panmanee, W. / Vattanaviboon, P. / Poole, L.B. / Mongkolsuk, S.
History
DepositionApr 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator OhrR
B: Transcriptional regulator OhrR


Theoretical massNumber of molelcules
Total (without water)33,8772
Polymers33,8772
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-29 kcal/mol
Surface area12620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.140, 98.260, 88.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsthe biological assembly is a dimer

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Components

#1: Protein Transcriptional regulator OhrR


Mass: 16938.436 Da / Num. of mol.: 2 / Mutation: C131S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: ohrR / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93R11
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 300mM magnesium chloride, 100 mM Tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 13, 2006 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→33.76 Å / Num. all: 20491 / Num. obs: 20477 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 14
Reflection shellResolution: 1.93→2 Å / Redundancy: 6.13 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2012 / Rsym value: 0.28 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å33.76 Å
Translation2.5 Å33.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: residues 18 to 107 from pdb entry 2PEX

2pex


Resolution: 1.93→33.76 Å / Rfactor Rfree error: 0.008 / FOM work R set: 0.84 / Data cutoff high absF: 1872286.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 995 4.9 %RANDOM
Rwork0.219 ---
obs0.219 20477 99.8 %-
all-20491 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.354 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2---1.74 Å20 Å2
3---3.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.93→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 0 84 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it2.881.5
X-RAY DIFFRACTIONc_mcangle_it3.732
X-RAY DIFFRACTIONc_scbond_it5.182
X-RAY DIFFRACTIONc_scangle_it7.562.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.93-1.970.347370.2610121049
1.97-20.28530.24410171070
2-2.040.296540.22710031057
2.04-2.090.258530.2059881041
2.09-2.140.237600.20110301090
2.14-2.190.27580.1919881046
2.19-2.250.24590.18910101069
2.25-2.320.268480.20510301078
2.32-2.390.221540.22810011055
2.39-2.480.292510.22110281079
2.48-2.580.272610.22710091070
2.58-2.690.284560.24210231079
2.69-2.830.333450.24110161061
2.83-3.010.24480.24210381086
3.01-3.240.252570.23910321089
3.24-3.570.279510.22310341085
3.57-4.090.237470.210581105
4.09-5.150.194520.18410551107
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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