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Yorodumi- PDB-1okr: Three-dimensional structure of S.aureus methicillin-resistance re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1okr | ||||||
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Title | Three-dimensional structure of S.aureus methicillin-resistance regulating transcriptional repressor MecI. | ||||||
Components | METHICILLIN RESISTANCE REGULATORY PROTEIN MECI | ||||||
Keywords | BACTERIAL ANTIBIOTIC RESISTANCE / MECI PROTEIN / TRANSCRIPTIONAL REGULATORY ELEMENT / DNA-BINDING PROTEIN / WINGED HELIX PROTEIN | ||||||
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 / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Garcia-Castellanos, R. / Marrero, A. / Mallorqui-Fernandez, G. / Potempa, J. / Coll, M. / Gomis-Ruth, F.X. | ||||||
Citation | 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-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1okr.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1okr.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 1okr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1okr_validation.pdf.gz | 381.6 KB | Display | wwPDB validaton report |
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Full document | 1okr_full_validation.pdf.gz | 384.6 KB | Display | |
Data in XML | 1okr_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1okr_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1okr ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1okr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.882, -0.283, 0.376), Vector: |
-Components
#1: Protein | Mass: 14812.003 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: N315 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P26598, UniProt: P68261*PLUS #2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 3.1 Å3/Da / Density % sol: 60 % Description: THE DATASETS ARE PART OF A 3-THREE WAVELENGTH MAD EXPERIMENT. THE WAVELENGTH OF THE NATIVE DATASET IS 0.97625 ANG. THE DATASET CONTAINS 14159 UNIQUE REFLECTIONS |
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Crystal grow | Temperature: 277 K / pH: 7.4 / Details: 20 MM TRIS-HCL PH 7.4, 0.2 M NACL AT 4 DEGREES. |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625,0.97915,0.97926, 0.96111 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→66.1 Å / Num. obs: 61498 / % possible obs: 96.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 5.6 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.4 / % possible all: 84.7 | |||||||||||||||
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 66.1 Å / Num. obs: 14159 / Num. measured all: 61498 / Rmerge(I) obs: 0.061 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 84.7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.895 / SU B: 9.736 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ADDITIONAL REFINEMENT WAS PERFORMED USING CNS 1.1.
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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: 30.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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