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Yorodumi- PDB-4i6u: Crystal Structure of a Y37F mutant of the Restriction-Modificatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i6u | ||||||
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Title | Crystal Structure of a Y37F mutant of the Restriction-Modification Controller Protein C.Esp1396I | ||||||
Components | Regulatory protein | ||||||
Keywords | TRANSCRIPTION / Restriction-modification / helix-turn-helix / transcriptional regulato / DNA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Martin, R.N.A. / McGeehan, J.E. / Kneale, G.G. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I. Authors: Martin, R.N. / McGeehan, J.E. / Kneale, G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of the restriction-modification controller protein C.Esp1396I. Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E. #2: Journal: Nucleic Acids Res. / Year: 2012 Title: Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex. Authors: McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G. #3: Journal: Nucleic Acids Res. / Year: 2012 Title: The structural basis of differential DNA sequence recognition by restriction-modification controller proteins. Authors: Ball, N.J. / McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G. #4: Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of the restriction-modification controller protein C.Esp1396I. Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i6u.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i6u.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 4i6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i6u_validation.pdf.gz | 494.1 KB | Display | wwPDB validaton report |
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Full document | 4i6u_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 4i6u_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4i6u_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6u ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6u | HTTPS FTP |
-Related structure data
Related structure data | 4f8dC 4fbiC 4fn3C 4i6rC 4i6tC 4ia8C 4ivzC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 9505.175 Da / Num. of mol.: 6 / Mutation: Y37F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. (bacteria) / Strain: RFL1396 / Gene: esp1396IC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8GGH0 |
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-Non-polymers , 5 types, 155 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M sodium sulphate, 0.2 M sodium acetate, 0.1 M Bis Tris propane, 20 % w/v PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 15, 2012 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→45.74 Å / Num. all: 527601 / Num. obs: 38881 / Rmerge(I) obs: 0.081 / Net I/σ(I): 22.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→41.79 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.063 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.08 Å2 / Biso mean: 23.0441 Å2 / Biso min: 9.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→41.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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