+Open data
-Basic information
Entry | Database: PDB / ID: 1vsm | ||||||
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Title | ASV INTEGRASE CORE DOMAIN IN CITRATE BUFFER PH 5.0 | ||||||
Components | PROTEIN (INTEGRASE) | ||||||
Keywords | HYDROLASE / ENDONUCLEASE / TRANSFERASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Lubkowski, J. / Yang, F. / Alexandratos, J. / Wlodawer, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Structural basis for inactivating mutations and pH-dependent activity of avian sarcoma virus integrase. Authors: Lubkowski, J. / Yang, F. / Alexandratos, J. / Merkel, G. / Katz, R.A. / Gravuer, K. / Skalka, A.M. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vsm.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vsm.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/1vsm ftp://data.pdbj.org/pub/pdb/validation_reports/vs/1vsm | HTTPS FTP |
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-Related structure data
Related structure data | 1vskC 1vslC 1asvS 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
#1: Protein | Mass: 15999.388 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin) Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: Schmidt-Ruppin / Plasmid: PRC23IN(52-207) / Production host: Escherichia coli (E. coli) References: UniProt: P03354, UniProt: O92956*PLUS, RNA-directed DNA polymerase |
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#2: 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 38 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.0, pH 5.6 | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Bujacz, G., (1995) J. Mol. Biol., 253, 333. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 9, 1998 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→20 Å / Num. obs: 9166 / % possible obs: 85.7 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rsym value: 0.08 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.13→2.19 Å / Mean I/σ(I) obs: 10 / Rsym value: 0.312 / % possible all: 86.5 |
Reflection | *PLUS Num. measured all: 28268 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 86.5 % / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ASV Resolution: 2.15→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
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Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.234 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.219 |