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- PDB-2pex: Structure of reduced C22S OhrR from Xanthamonas Campestris -

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Basic information

Entry
Database: PDB / ID: 2pex
TitleStructure of reduced C22S OhrR from Xanthamonas Campestris
ComponentsTranscriptional regulator OhrR
KeywordsTRANSCRIPTION REGULATOR
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / 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 ...: / 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
FORMIC ACID / MarR family transcriptional regulator
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SAD / MAD / Resolution: 1.9 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 3, 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 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1999
Polymers33,8772
Non-polymers3227
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-48 kcal/mol
Surface area13380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.290, 77.790, 77.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: C22S
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: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 4M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceTypeIDWavelength
ROTATING ANODERIGAKU11.54
ROTATING ANODERIGAKU22.29
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS1IMAGE PLATEMar 10, 2006mirrors
RIGAKU RAXIS2IMAGE PLATEApr 12, 2006mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.291
ReflectionRedundancy: 26.69 % / Av σ(I) over netI: 42.1 / Number: 359108 / Rmerge(I) obs: 0.061 / Χ2: 0.94 / D res high: 2.4 Å / D res low: 27.63 Å / Num. obs: 13353 / % possible obs: 99.4
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
5.1627.6399.70.0481.4425.311316
4.15.161000.0521.0927.49120
3.584.11000.0570.9327.6633
3.263.581000.0610.927.4855
3.023.2699.90.0680.8927.37113
2.853.0299.60.0810.8727.03162
2.72.8599.50.0940.8626.98200
2.592.798.40.1110.8226.74325
2.492.5998.60.1250.826.5202
2.42.4997.90.1360.7624.35168
ReflectionResolution: 1.9→25.63 Å / Num. all: 26612 / Num. obs: 26616 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 13.79 % / Biso Wilson estimate: 34.1 Å2 / Limit h max: 28 / Limit h min: 0 / Limit k max: 40 / Limit k min: 0 / Limit l max: 40 / Limit l min: 0 / Observed criterion F max: 1160314.12 / Observed criterion F min: 2.5 / Rmerge(I) obs: 0.063 / Χ2: 0.98 / Net I/σ(I): 20.4 / Scaling rejects: 2773
Reflection shell

Diffraction-ID: 1,2 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2
1.9-1.9713.590.4014.63544126030.96
1.97-2.0513.630.3215.83602626350.97
2.05-2.1413.620.2647.13551325931.05
2.14-2.2513.740.2168.73643426361.02
2.25-2.3913.80.1810.63656926350.97
2.39-2.5813.970.14612.53722826520.94
2.58-2.8414.070.108173743326470.9
2.84-3.2514.10.06826.83798226810.84
3.25-4.0914.040.04340.63838927100.93
4.09-25.6313.30.0366.83868228241.19

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1S14.9840.0390.0020.0630.906
2S14.4130.4540.6240.1311.006
3S26.470.2720.8610.1671.183
4S23.360.8980.2650.1420.927
5S600.4960.8290.1970.755
6S43.9950.1610.1020.0930.663
7S3.6770.3910.9460.1490.247
Phasing dmFOM : 0.71 / FOM acentric: 0.73 / FOM centric: 0.59 / Reflection: 11820 / Reflection acentric: 10091 / Reflection centric: 1729
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-27.6260.850.930.71562366196
4.5-7.10.860.890.7516251285340
3.6-4.50.860.880.7519951692303
3.1-3.60.80.820.6319991727272
2.7-3.10.650.680.4335083104404
2.5-2.70.440.460.2621311917214

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
CNS1.2refinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→25.63 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 1160314.125 / 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
Rfree0.278 2640 9.9 %RANDOM
Rwork0.236 ---
obs0.236 26612 99.8 %-
all-26622 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.588 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 68.5 Å2 / Biso mean: 32.8 Å2 / Biso min: 18.04 Å2
Baniso -1Baniso -2Baniso -3
1-8.65 Å20 Å20 Å2
2---5.09 Å20 Å2
3----3.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→25.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 21 175 2323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_torsion_deg18.8
X-RAY DIFFRACTIONc_torsion_impr_deg0.7
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.37733610.30.34429180.0213264325499.7
1.99-2.090.32234310.40.27129540.0173304329799.8
2.09-2.220.296325100.24329410.0163272326699.8
2.22-2.390.2853239.80.23929580.0163285328199.9
2.39-2.630.28133510.10.26229800.0153318331599.9
2.63-3.010.3123139.40.27230180.01833323331100
3.01-3.80.2834910.40.22930150.0153366336499.9
3.8-25.630.23631690.20131880.0133507350499.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3fmt_par.txtfmt_top.txt

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