[English] 日本語
![](img/lk-miru.gif)
- PDB-1vsd: ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1vsd | ||||||
---|---|---|---|---|---|---|---|
Title | ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, HIGH MG CONCENTRATION FORM | ||||||
![]() | INTEGRASE | ||||||
![]() | ENDORIBONUCLEASE / HYDROLASE / ENDONUCLEASE | ||||||
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. / Jaskolski, M. / Alexandratos, J. / Wlodawer, A. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 48.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 33 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 385.8 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
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: 16767.285 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 500 MILLIMOLAR MGCL2 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 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: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-EPE / |
#4: 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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.78 % |
---|---|
Crystal grow | pH: 7.5 Details: pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLI-MOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 500 MILLI-MOLAR MGCL2. |
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ![]() |
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: 19297 / % possible obs: 99.8 % / Redundancy: 4.88 % / Rmerge(I) obs: 0.064 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Rmerge(I) obs: 0.064 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.7→8 Å / σ(F): 2 Details: THE CLOSE (LESS THAN 2.5 ANGSTROMS) CONTACTS AT 146 ILE N - 148 ASN O (MAIN-MAIN) AND 149 ASN O - 151 GLN N (MAIN-MAIN) ARE LOCATED IN THE LEAST RELIABLE PART OF THE MODEL, A FLEXIBLE LOOP ...Details: THE CLOSE (LESS THAN 2.5 ANGSTROMS) CONTACTS AT 146 ILE N - 148 ASN O (MAIN-MAIN) AND 149 ASN O - 151 GLN N (MAIN-MAIN) ARE LOCATED IN THE LEAST RELIABLE PART OF THE MODEL, A FLEXIBLE LOOP REGION. THE QUALITY OF THE ELECTRON DENSITY AND THE RELATIVELY HIGHER B-FACTORS IN THIS SHORT SECTION OF THE SEQUENCE RESULTED IN POORER FINAL REFINEMENT THAN FOR THE REST OF THIS STRUCTURE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|