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Open data
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Basic information
Entry | Database: PDB / ID: 1vsi | ||||||
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Title | ASV INTEGRASE CORE DOMAIN WITH CA(II) COFACTOR | ||||||
![]() | INTEGRASE | ||||||
![]() | ENDONUCLEASE / HYDROLASE / ENDORIBONUCLEASE / RNA-DIRECTED DNA POLYMERASE | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Bujacz, G. / Alexandratos, J. / Wlodawer, A. | ||||||
![]() | ![]() Title: Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity. Authors: Bujacz, G. / Alexandratos, J. / Wlodawer, A. / Merkel, G. / Andrake, M. / Katz, R.A. / Skalka, A.M. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1VSF | ||||||
Remark 700 | SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1VSF |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.1 KB | Display | ![]() |
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PDB format | ![]() | 31.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.1 KB | Display | ![]() |
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Full document | ![]() | 437.3 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | THE BIOLOGICALLY ACTIVE MOLECULE IS A DIMER. |
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Components
#1: Protein | Mass: 16767.285 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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 Plasmid: PRC23IN(52-207) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-EPE / |
#4: Water | ChemComp-HOH / |
Sequence details | ALA 101, VIRAL STRAIN DIFFERENCES LYS 166, VIRAL STRAIN DIFFERENCES REFERENCE: THE APPARENT ...ALA 101, VIRAL STRAIN DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 38 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM CACL2. | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 8, 1996 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 9230 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.11 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.05 / Rsym value: 0.375 / % possible all: 92.1 |
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Processing
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Refinement | Method to determine structure: ISOSTRUCTURAL TO PDB ENTRY 1VSF Resolution: 2.2→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |