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Yorodumi- PDB-1asw: AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1asw | ||||||
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Title | AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, HEPES PH 7.5 USING SELENOMETHIONINE SUBSTITUTED PROTEIN; DATA COLLECTED AT-165 DEGREES C | ||||||
Components | AVIAN SARCOMA VIRUS INTEGRASE | ||||||
Keywords | DNA INTEGRATION | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / RNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Avian sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: High-resolution structure of the catalytic domain of avian sarcoma virus integrase. Authors: Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Katz, R.A. / Skalka, A.M. #1: Journal: J.Biol.Chem. / Year: 1990 Title: Expression, Purification, and Crystallization of Natural and Selenomethionyl Recombinant Ribonuclease H from Escherichia Coli Authors: Yang, W. / Hendrickson, W.A. / Kalman, E.T. / Crouch, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1asw.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1asw.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 1asw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/1asw ftp://data.pdbj.org/pub/pdb/validation_reports/as/1asw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 73 |
-Components
#1: Protein | Mass: 18083.082 Da / Num. of mol.: 1 Mutation: INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209) Source method: isolated from a genetically manipulated source Details: CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, HEPES PH 7.5 USING SELENOMETHIONINE-SUBSTITUTED PROTEIN, DATA COLLECTED AT LOW TEMPERATURE Source: (gene. exp.) Avian sarcoma virus / Genus: Alpharetrovirus / Strain: SCHMIDT-RUPPIN B / Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli) / References: UniProt: P03354, UniProt: O92956*PLUS |
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#2: Chemical | ChemComp-EPE / |
#3: Chemical | ChemComp-IPA / |
#4: Water | ChemComp-HOH / |
Source details | ORIGINAL VIRAL DNA CLONE: JU ET AL., J. VIROL. 33:1026-1033 (1980) ORIGINAL EXPRESSION CLONE: TERRY ...ORIGINAL VIRAL DNA CLONE: JU ET AL., J. VIROL. 33:1026-1033 (1980) ORIGINAL EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.24 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9464, 0.9792, 0.9790 | ||||||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 10, 1995 | ||||||||||||
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→25 Å / Num. obs: 12157 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 7.07 % / Rmerge(I) obs: 0.068 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.068 |
-Processing
Software |
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Refinement | Resolution: 1.8→6 Å / σ(F): 2
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Displacement parameters | Biso mean: 18.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |