[English] 日本語
Yorodumi- PDB-4i6t: Crystal Structure of a T36A mutant of the Restriction-Modificatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i6t | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a T36A mutant of the Restriction-Modification Controller Protein C.Esp1396I | ||||||
Components | Regulatory protein | ||||||
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: 2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4i6t.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4i6t.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 4i6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i6t_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4i6t_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 4i6t_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 4i6t_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6t ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6t | HTTPS FTP |
-Related structure data
Related structure data | 4f8dC 4fbiC 4fn3C 4i6rC 4i6uC 4ia8C 4ivzC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 77 / Label seq-ID: 6 - 80
| ||||||||||||||||||
Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 9491.148 Da / Num. of mol.: 2 / Mutation: T36A 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 | ChemComp-MLI / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM Sodium Sulphate, 2.4 M Sodium Malonate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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→56.681 Å / Num. all: 130244 / Num. obs: 12508 / % possible obs: 99.6 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.437 / Net I/σ(I): 4.2 | ||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.026 / Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2521 / WRfactor Rwork: 0.192 / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8349 / SU B: 5.037 / SU ML: 0.134 / SU R Cruickshank DPI: 0.1753 / SU Rfree: 0.1704 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 80.32 Å2 / Biso mean: 28.8705 Å2 / Biso min: 9.08 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 4415 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.2 Å / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
|