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Yorodumi- PDB-4fbi: Crystal Structure of an R46A mutant of the Restriction-Modificati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fbi | ||||||
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Title | Crystal Structure of an R46A mutant of the Restriction-Modification Controller Protein C.Esp1396I (Trigonal Form) | ||||||
Components | Regulatory proteinRegulation of gene expression | ||||||
Keywords | TRANSCRIPTION / Restriction-modification / helix-turn-helix / transcriptional regulator / DNA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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: Nucleic Acids Res. / Year: 2008 Title: Structural analysis of the genetic switch that regulates the expression of restriction-modification genes. Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Ball, N. / Ravelli, R.B. / Kneale, G.G. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fbi.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fbi.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/4fbi ftp://data.pdbj.org/pub/pdb/validation_reports/fb/4fbi | HTTPS FTP |
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-Related structure data
Related structure data | 4f8dC 4fn3C 4i6rC 4i6tC 4i6uC 4ia8C 4ivzC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9435.059 Da / Num. of mol.: 4 / Mutation: R46A 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 #2: Chemical | #3: 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: 2.33 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M MIB buffer, 25% w/v PEG 1500, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979494 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979494 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.487→71.38 Å / Num. all: 53279 / Num. obs: 53279 / % possible obs: 95.1 % / Redundancy: 2.4 % / Rsym value: 0.034 / Net I/σ(I): 15.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.19 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1939 / WRfactor Rwork: 0.1566 / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8951 / SU B: 0.003 / SU ML: 0 / SU R Cruickshank DPI: 0.0699 / SU Rfree: 0.0761 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 79.27 Å2 / Biso mean: 16.4158 Å2 / Biso min: 5.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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