+Open data
-Basic information
Entry | Database: PDB / ID: 1sd6 | ||||||
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Title | Crystal Structure of Native MecI at 2.65 A | ||||||
Components | Methicillin resistance regulatory protein mecI | ||||||
Keywords | DNA BINDING PROTEIN / BlaI / MecI / repressor / methicillin / B-lactam | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.65 Å | ||||||
Authors | Safo, M.K. / Zhao, Q. / Musayev, F.N. / Robinson, H. / Scarsdale, N. / Archer, G.L. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2005 Title: Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons Authors: Safo, M.K. / Zhao, Q. / Ko, T.-P. / Musayev, F.N. / Robinson, H. / Scarsdale, N. / Wang, A.H.-J. / Archer, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sd6.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sd6.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 1sd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sd6_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 1sd6_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 1sd6_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1sd6_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/1sd6 ftp://data.pdbj.org/pub/pdb/validation_reports/sd/1sd6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains the biological homodimer |
-Components
#1: Protein | Mass: 14826.030 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: MECI, SA0040 / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P68262 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.23 % | |||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, Sodium Cacodylate, Magnesium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 12, 2001 / Details: mirrors |
Radiation | Monochromator: MSC Confocal Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→36.48 Å / Num. all: 9536 / Num. obs: 9418 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1180 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.65→32.61 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 91660.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.5 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.1141 Å2 / ksol: 0.311292 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→32.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Refine LS restraints | *PLUS
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