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Yorodumi- PDB-6t71: 3C-like protease from Southampton virus complexed with XST00000375b. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t71 | ||||||
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Title | 3C-like protease from Southampton virus complexed with XST00000375b. | ||||||
Components | (Genome polyprotein) x 2 | ||||||
Keywords | HYDROLASE / Viral protease. | ||||||
Function / homology | Function and homology information calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell endoplasmic reticulum membrane / 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 / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Southampton virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 Å | ||||||
Authors | Guo, J. / Cooper, J.B. | ||||||
Citation | Journal: J Struct Biol X / Year: 2020 Title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors. Authors: Guo, J. / Douangamath, A. / Song, W. / Coker, A.R. / Chan, A.W.E. / Wood, S.P. / Cooper, J.B. / Resnick, E. / London, N. / Delft, F.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t71.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t71.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 6t71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t71_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6t71_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6t71_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 6t71_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/6t71 ftp://data.pdbj.org/pub/pdb/validation_reports/t7/6t71 | HTTPS FTP |
-Related structure data
Related structure data | 6t1qSC 6t2iC 6t2xC 6t3gC 6t49C 6t4eC 6t4sC 6t5dC 6t5rC 6t6wC 6t82C 6t8rC 6t8tC 6talC 6tawC 6tboC 6tbpC 6tc1C 6tcfC 6tglC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 18387.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Southampton virus (serotype 3) / Gene: ORF1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase |
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#2: Protein | Mass: 18290.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Southampton virus (serotype 3) / Gene: ORF1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q04544, nucleoside-triphosphate phosphatase, calicivirin, RNA-directed RNA polymerase |
-Non-polymers , 4 types, 356 molecules
#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: Protein concentration 4 mg/ml. 0.2 M ammonium citrate and 12% (v/v) PEG3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2016 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.52→60.95 Å / Num. obs: 51832 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.031 / Rrim(I) all: 0.056 / Net I/σ(I): 9.6 / Num. measured all: 162852 / Scaling rejects: 10 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6t1q Resolution: 1.52→60.93 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.791 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0799 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.077 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ANISOTROPIC U VALUES : REFINED INDIVIDUALLY
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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 max: 127.96 Å2 / Biso mean: 27.703 Å2 / Biso min: 9.7 Å2
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Refinement step | Cycle: final / Resolution: 1.52→60.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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