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- PDB-4f8d: Crystal Structure of an R46A mutant of the Restriction-Modificati... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f8d | ||||||
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Title | Crystal Structure of an R46A mutant of the Restriction-Modification Controller Protein C.Esp1396I (Monoclinic Form) | ||||||
![]() | Regulatory protein | ||||||
![]() | TRANSCRIPTION / Restriction-modification / Helix-Turn-Helix / Transcriptional Regulator / DNA | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Martin, R.N.A. / McGeehan, J.E. / Kneale, G.G. | ||||||
![]() | ![]() Title: Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I. Authors: Martin, R.N. / McGeehan, J.E. / Kneale, G. #1: ![]() 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: ![]() Title: Structure of the restriction-modification controller protein C.Esp1396I. Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E. #3: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51 KB | Display | ![]() |
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PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452 KB | Display | ![]() |
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Full document | ![]() | 455.5 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fbiC ![]() 4fn3C ![]() 4i6rC ![]() 4i6tC ![]() 4i6uC ![]() 4ia8C ![]() 4ivzC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.: 2 / Mutation: R46A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 200mM Sodium Sulphate, 20% PEG 3350, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.5→24.7 Å / Num. all: 90345 / Num. obs: 27204 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.014 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.31 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
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Processing
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Refinement | Method to determine structure: ![]() 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: 61.55 Å2 / Biso mean: 18.566 Å2 / Biso min: 6.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→24.7 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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