[English] 日本語
Yorodumi- PDB-2uut: The 2.4 angstrom resolution structure of the D346G mutant of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uut | ||||||
---|---|---|---|---|---|---|---|
Title | The 2.4 angstrom resolution structure of the D346G mutant of the Sapporo Virus RdRp polymerase | ||||||
Components | RNA-DIRECTED RNA POLYMERASERNA-dependent RNA polymerase | ||||||
Keywords | HYDROLASE / NUCLEOTIDE-BINDING / NUCLEOTIDYLTRANSFERASE / COVALENT PROTEIN-RNA LINKAGE / POLYMERASE / RNA ELONGATION / TRANSFERASE ACTIVITY / MUTANT / CAPSID PROTEIN / RNA REPLICATION / STRUCTURAL PROTEIN / PROTEASE / HELICASE / TRANSFERASE / RNA-DIRECTED RNA POLYMERASE / POLYPROTEIN / ATP-BINDING / THIOL PROTEASE | ||||||
Function / homology | Function and homology information calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / DNA replication / host cell cytoplasm / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity ...calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / DNA replication / host cell cytoplasm / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | SAPPORO VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Fullerton, S.W.B. / Robel, I. / Schuldt, L. / Gebhardt, J. / Tucker, P. / Rohayem, J. | ||||||
Citation | Journal: To be Published Title: The 2.4 Angstrom Resolution Structure of the D346G Mutant of the Sapporo Virus Rdrp Polymerase Authors: Fullerton, S.W.B. / Robel, I. / Schuldt, L. / Gebhardt, J. / Tucker, P. / Rohayem, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2uut.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2uut.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 2uut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/2uut ftp://data.pdbj.org/pub/pdb/validation_reports/uu/2uut | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ckwS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 55739.949 Da / Num. of mol.: 1 Fragment: RNA POLYMERASE, RESIDUES 1135-1511,1518-1630,1632-1649 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SAPPORO VIRUS / Strain: SAPPORO / Tissue: INTESTINE / Description: FROM DRESDEN CALICI-LABORATORY / Variant: DRESDEN ISOLATE / Plasmid: PET M11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q69014, RNA-directed RNA polymerase |
---|---|
#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.62 % / Description: NONE |
---|---|
Crystal grow | pH: 6.8 / Details: pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8142 |
Detector | Type: MARREASEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8142 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→24 Å / Num. obs: 24268 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.42→2.57 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CKW Resolution: 2.4→22.27 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.866 / SU B: 7.584 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.281 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→22.27 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|