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- PDB-3t8t: Crystal structure of Staphylococcus aureus CymR oxidized form -

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Basic information

Entry
Database: PDB / ID: 3t8t
TitleCrystal structure of Staphylococcus aureus CymR oxidized form
ComponentsStaphylococcus aureus CymR (oxidized form)
KeywordsUNKNOWN FUNCTION / Transcriptional regulator protein / Dimer / sulfenic acid
Function / homology
Function and homology information


Transcription regulator Rrf2-type, conserved site / Rrf2-type HTH domain signature. / Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / 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
Rrf2 family transcriptional regulator / Uncharacterized protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsHe, C. / Ji, Q.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Staphylococcus aureus CymR Is a New Thiol-based Oxidation-sensing Regulator of Stress Resistance and Oxidative Response.
Authors: Ji, Q. / Zhang, L. / Sun, F. / Deng, X. / Liang, H. / Bae, T. / He, C.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Staphylococcus aureus CymR (oxidized form)


Theoretical massNumber of molelcules
Total (without water)15,9481
Polymers15,9481
Non-polymers00
Water1,06359
1
A: Staphylococcus aureus CymR (oxidized form)

A: Staphylococcus aureus CymR (oxidized form)


Theoretical massNumber of molelcules
Total (without water)31,8962
Polymers31,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3220 Å2
ΔGint-24 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.328, 52.576, 33.449
Angle α, β, γ (deg.)90.00, 98.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Staphylococcus aureus CymR (oxidized form)


Mass: 15948.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: SAV1626 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99TM3, UniProt: A0A0H3JRR0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Lithium sulfate monohydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 12% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.752→19.138 Å / Num. all: 13422 / Num. obs: 13355
Reflection shellResolution: 1.752→1.81 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.752→19.138 Å / SU ML: 0.27 / σ(F): 0.05 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 2324 9.92 %
Rwork0.2136 --
obs0.2173 13355 89.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.098 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2465 Å2-0 Å28.9823 Å2
2---0.0749 Å20 Å2
3----2.1716 Å2
Refinement stepCycle: LAST / Resolution: 1.752→19.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 0 59 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007973
X-RAY DIFFRACTIONf_angle_d1.0461307
X-RAY DIFFRACTIONf_dihedral_angle_d14.337382
X-RAY DIFFRACTIONf_chiral_restr0.079151
X-RAY DIFFRACTIONf_plane_restr0.006167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.752-1.81490.34891840.29081645X-RAY DIFFRACTION71
1.8149-1.88750.32421940.28921861X-RAY DIFFRACTION77
1.8875-1.97330.31052100.26591961X-RAY DIFFRACTION83
1.9733-2.07720.33162280.23152092X-RAY DIFFRACTION88
2.0772-2.20720.2812350.2062093X-RAY DIFFRACTION90
2.2072-2.37730.26332480.20822208X-RAY DIFFRACTION94
2.3773-2.6160.24272450.21012244X-RAY DIFFRACTION95
2.616-2.99330.23422580.21142297X-RAY DIFFRACTION97
2.9933-3.76660.22122610.20312334X-RAY DIFFRACTION99
3.7666-19.13950.22112610.19522366X-RAY DIFFRACTION100

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