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Yorodumi- PDB-7h95: Group deposition for crystallographic fragment screening of Chiku... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7h95 | ||||||
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Title | Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z239125320 (CHIKV_MacB-x1372) | ||||||
Components | Non-structural protein 3 | ||||||
Keywords | VIRAL PROTEIN / Diamond Light Source / I04-1 / READDI / Chikungunya Virus / crystallographic fragment screening / PanDDA / XChemExplorer | ||||||
Function / homology | Function and homology information host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Chikungunya virus Chikungunya Virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. ...Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / von Delft, F. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain Authors: Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / ...Authors: Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / von Delft, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7h95.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7h95.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 7h95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/7h95 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/7h95 | HTTPS FTP |
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-Group deposition
ID | G_1002294 (109 entries) |
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Title | Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain |
Type | changed state |
Description | Crystallographic fragment screening of Chikungunya virus nsP3 macrodomain |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 17819.215 Da / Num. of mol.: 4 / Fragment: macrodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli (E. coli) References: UniProt: Q8JUX6, ADP-ribose 1''-phosphate phosphatase |
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-Non-polymers , 5 types, 577 molecules
#2: Chemical | ChemComp-DMS / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-5MK / #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: 2.62 Å3/Da / Density % sol: 53.11 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 13, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92124 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→56.53 Å / Num. obs: 116069 / % possible obs: 98 % / Redundancy: 10.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.028 / Rrim(I) all: 0.088 / Χ2: 0.59 / Net I/σ(I): 15.4 / Num. measured all: 1203951 |
Reflection shell | Resolution: 1.49→1.52 Å / % possible obs: 96.4 % / Redundancy: 8.1 % / Rmerge(I) obs: 2.059 / Num. measured all: 45649 / Num. unique obs: 5654 / CC1/2: 0.363 / Rpim(I) all: 0.763 / Rrim(I) all: 2.2 / Χ2: 0.18 / Net I/σ(I) obs: 0.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→56.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.958 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.128 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→56.6 Å
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