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Yorodumi- PDB-1vse: ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vse | ||||||
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Title | ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM | ||||||
Components | INTEGRASE | ||||||
Keywords | ENDORIBONUCLEASE / HYDROLASE / ENDONUCLEASE | ||||||
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 | Rous sarcoma virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. | ||||||
Citation | Journal: Structure / Year: 1996 Title: The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations. Authors: Bujacz, G. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Katz, R.A. / Skalka, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vse.cif.gz | 45.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vse.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/1vse ftp://data.pdbj.org/pub/pdb/validation_reports/vs/1vse | 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 | ||||||||
Details | THIS FILE CONTAINS ONLY A MONOMER. IN ORDER TO CREATE THE SECOND SUBUNIT OF THE DIMERIC MOLECULE, THE FRACTIONAL CRYSTALLOGRAPHIC COORDINATES NEED TO BE TRANSFORMED BY Y, X, 1.0 - Z. |
-Components
#1: Protein | Mass: 16723.232 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209 Source method: isolated from a genetically manipulated source Details: CRYSTALS SOAKED IN 20 MILLIMOILAR MGCL2 Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin) Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: Schmidt-Ruppin Description: ORIGINAL VIRAL DNA CLONE\: JU ET AL., J. VIROL. 33:1026-1033 (1980), ORIGINAL EXPRESSION CLONE\: TERRY ET AL., J. VIROL. 62:2358-2365 (1988), EXPRESSION CLONE FOR CORE\: KULKOSKY ET AL., ...Description: ORIGINAL VIRAL DNA CLONE\: JU ET AL., J. VIROL. 33:1026-1033 (1980), ORIGINAL EXPRESSION CLONE\: TERRY ET AL., J. VIROL. 62:2358-2365 (1988), EXPRESSION CLONE FOR CORE\: KULKOSKY ET AL., J. VIROL. 206:448-456 (1995) 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: Water | ChemComp-HOH / |
Sequence details | THE APPARENT DISCREPANCY BETWEEN THE SEQUENCE PRESENTED HERE AND THE "POL_RSVP" SEQUENCE IS A ...THE APPARENT DISCREPANC |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % |
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Crystal grow | pH: 7.5 Details: pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLIMOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 20 MILLIMOLAR MGCL2. |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 30, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 9523 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 5.28 % / Rmerge(I) obs: 0.111 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Rmerge(I) obs: 0.111 |
-Processing
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Refinement | Resolution: 2.2→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 22.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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