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Yorodumi- PDB-1sax: Three-dimensional structure of s.aureus methicillin-resistance re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sax | ||||||
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Title | Three-dimensional structure of s.aureus methicillin-resistance regulating transcriptional repressor meci in complex with 25-bp ds-DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / winged helix-turn-helix / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Garcia-Castellanos, R. / Mallorqui-Fernandez, G. / Marrero, A. / Potempa, J. / Coll, M. / Gomis-Ruth, F.X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: On the transcriptional regulation of methicillin resistance: MecI repressor in complex with its operator Authors: Garcia-Castellanos, R. / Mallorqui-Fernandez, G. / Marrero, A. / Potempa, J. / Coll, M. / Gomis-Ruth, F.X. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Three-dimensional structure of MecI. Molecular basis for transcriptional regulation of staphylococcal methicillin resistance Authors: Garcia-Castellanos, R. / Marrero, A. / Mallorqui-Fernandez, G. / Potempa, J. / Coll, M. / Gomis-Rueth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sax.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sax.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sax_validation.pdf.gz | 385.9 KB | Display | wwPDB validaton report |
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Full document | 1sax_full_validation.pdf.gz | 398.4 KB | Display | |
Data in XML | 1sax_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1sax_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/1sax ftp://data.pdbj.org/pub/pdb/validation_reports/sa/1sax | HTTPS FTP |
-Related structure data
Related structure data | 1okrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 7653.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MecI operator sequence | ||||
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#2: DNA chain | Mass: 7699.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MecI operator sequence | ||||
#3: Protein | Mass: 14812.003 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Species: Staphylococcus aureus / Strain: N315 / Gene: mecI / Plasmid: pProEX Hta (Invitrogen) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P68262, UniProt: P68261*PLUS #4: Chemical | ChemComp-K / | #5: 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: 3.1 Å3/Da / Density % sol: 60.28 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9789 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: liq. N2 cooled Si-111 double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→39.7 Å / Num. all: 14087 / Num. obs: 13777 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 86.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.3 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Starting model: 1OKR Resolution: 2.8→39.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.874 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.501 / ESU R Free: 0.39
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→39.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20 /
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