+Open data
-Basic information
Entry | Database: PDB / ID: 3t8t | ||||||
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Title | Crystal structure of Staphylococcus aureus CymR oxidized form | ||||||
Components | Staphylococcus aureus CymR (oxidized form) | ||||||
Keywords | UNKNOWN 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 | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å | ||||||
Authors | He, C. / Ji, Q. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t8t.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t8t.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 3t8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t8t_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 3t8t_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 3t8t_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 3t8t_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/3t8t ftp://data.pdbj.org/pub/pdb/validation_reports/t8/3t8t | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.72 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.752→19.138 Å / Num. all: 13422 / Num. obs: 13355 |
Reflection shell | Resolution: 1.752→1.81 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage 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 |
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Refinement step | Cycle: LAST / Resolution: 1.752→19.138 Å
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Refine LS restraints |
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LS refinement shell |
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