[English] 日本語
Yorodumi- PDB-6ff0: Ryegrass mottle virus serine protease domain fused with VPg domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ff0 | ||||||
---|---|---|---|---|---|---|---|
Title | Ryegrass mottle virus serine protease domain fused with VPg domain | ||||||
Components | Serine protease domain fused with VPg domain | ||||||
Keywords | VIRAL PROTEIN / serine protease / viral protease / viral polypeptide / viral genome-linked protein | ||||||
Function / homology | Function and homology information host cell membrane / serine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleotide binding / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | Ryegrass mottle virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kalnins, G. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2023 Title: VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure. Authors: Kalnins, G. / Ludviga, R. / Kalnciema, I. / Resevica, G. / Zeltina, V. / Bogans, J. / Tars, K. / Zeltins, A. / Balke, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ff0.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ff0.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ff0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ff0_validation.pdf.gz | 424.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ff0_full_validation.pdf.gz | 424.8 KB | Display | |
Data in XML | 6ff0_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 6ff0_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/6ff0 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/6ff0 | HTTPS FTP |
-Related structure data
Related structure data | 6fezC 7yzvC 1zyoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29509.355 Da / Num. of mol.: 1 / Fragment: UNP residues 119-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ryegrass mottle virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0MCW0, RNA-directed RNA polymerase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M MIB, pH 9.0, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.96411 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96411 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→74.08 Å / Num. obs: 11945 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1699 / CC1/2: 0.924 / Rpim(I) all: 0.17 / Rrim(I) all: 0.417 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZYO Resolution: 2.1→49.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.182 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.683 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→49.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|