+Open data
-Basic information
Entry | Database: PDB / ID: 6fez | ||||||
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Title | Ryegrass mottle virus protease domain | ||||||
Components | Serine protease domain | ||||||
Keywords | VIRAL PROTEIN / serine protease / viral protease | ||||||
Function / homology | Function and homology information host cell membrane / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / nucleotide binding / DNA-templated transcription / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | Ryegrass mottle virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fez.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fez.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 6fez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/6fez ftp://data.pdbj.org/pub/pdb/validation_reports/fe/6fez | HTTPS FTP |
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-Related structure data
Related structure data | 6ff0C 7yzvC 1zyoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20883.982 Da / Num. of mol.: 2 / Fragment: serine protease domain, UNP residues 119-317 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES 7.5, 22.5% PEG 3350, 0.22M LiSO4, 3% DMSO |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57.99 Å / Num. obs: 19160 / % possible obs: 95.98 % / Redundancy: 3 % / Biso Wilson estimate: 45.496 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.083 / Rrim(I) all: 0.149 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2981 / CC1/2: 0.644 / Rpim(I) all: 0.365 / Rrim(I) all: 0.662 / % possible all: 98.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZYO Resolution: 2.3→57.99 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.266 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.366 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→57.99 Å
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Refine LS restraints |
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