+Open data
-Basic information
Entry | Database: PDB / ID: 3evz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Methyltransferase from Pyrococcus furiosus | ||||||
Components | methyltransferase | ||||||
Keywords | TRANSFERASE / 11120i / Methyltransferase / NYSGXRC / New York SGX Research Center for Structural Genomics / Protein Structure Initiative / Pyrococcus furiosus / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Zhang, Z. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of methyltransferase from Pyrococcus furiosus Authors: Zhang, Z. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3evz.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3evz.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 3evz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3evz_validation.pdf.gz | 426 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3evz_full_validation.pdf.gz | 431.8 KB | Display | |
Data in XML | 3evz_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3evz_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/3evz ftp://data.pdbj.org/pub/pdb/validation_reports/ev/3evz | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26246.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0847 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q8U2I7 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.57 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: D9. 0.1 M Tris pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→55.22 Å / Num. all: 11261 / Num. obs: 10605 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.4 % / Rmerge(I) obs: 0.111 / Rsym value: 0.114 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 27.2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 8.6 / Rsym value: 0.342 / % possible all: 85 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.2→55.22 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.973 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 33.206 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→55.22 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 15.699 Å / Origin y: 8.171 Å / Origin z: -14.643 Å
|