[English] 日本語
Yorodumi- PDB-3i9f: Crystal structure of a putative type 11 methyltransferase from Su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i9f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a putative type 11 methyltransferase from Sulfolobus solfataricus | ||||||
Components | Putative type 11 methyltransferase | ||||||
Keywords | TRANSFERASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Bonanno, J.B. / Dickey, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a putative type 11 methyltransferase from Sulfolobus solfataricus Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3i9f.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3i9f.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 3i9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i9f_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3i9f_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 3i9f_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3i9f_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/3i9f ftp://data.pdbj.org/pub/pdb/validation_reports/i9/3i9f | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
2 |
| |||||||||||||||
3 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
| |||||||||||||||
Details | Probable biological dimer, crystallographic hexamer mediated by His6 tag and Zn |
-Components
#1: Protein | Mass: 19878.766 Da / Num. of mol.: 2 / Fragment: sequence database residues 18-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO1178 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97YX4 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.1 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7 Details: 20% PEG 3350, 200mM potassium nitrate, pH 7.0, vapor diffusion, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→36.913 Å / Num. all: 18652 / Num. obs: 18652 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.9 % / Biso Wilson estimate: 53.8 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 19 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2682 / Rsym value: 0.803 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.842 / SU B: 7.683 / SU ML: 0.176 / SU R Cruickshank DPI: 0.351 / SU Rfree: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.351 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; METALS MODELED AS ZN BASED ON ANOMALOUS DIFFERENCE FOURIER PEAKS AND GEOMETRY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 80.92 Å2 / Biso mean: 48.937 Å2 / Biso min: 21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
|