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- PDB-2x6n: Human foamy virus integrase - catalytic core. Manganese-bound str... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x6n | ||||||
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Title | Human foamy virus integrase - catalytic core. Manganese-bound structure. | ||||||
![]() | INTEGRASE | ||||||
![]() | VIRAL PROTEIN / RETROVIRAL INTEGRASE / DNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / DNA INTEGRATION / ASPARTYL PROTEASE / DNA RECOMBINATION / TRANSFERASE / NUCLEASE / HYDROLASE | ||||||
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 / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell ...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 / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rety, S. / Delelis, O. / Rezabkova, L. / Dubanchet, B. / Silhan, J. / Lewit-Bentley, A. | ||||||
![]() | ![]() Title: Structural Studies of the Catalytic Core of the Primate Foamy Virus (Pfv-1) Integrase Authors: Rety, S. / Rezabkova, L. / Dubanchet, B. / Silhan, J. / Legrand, P. / Lewit-Bentley, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.8 KB | Display | ![]() |
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PDB format | ![]() | 185.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2x6sC ![]() 2x74SC ![]() 2x78C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22577.797 Da / Num. of mol.: 6 / Fragment: CATALYTIC CORE, RESIDUES 861-1060 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ILE 878 TO MET ENGINEERED RESIDUE IN CHAIN A, ILE 978 TO MET ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.03 % / Description: NONE |
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Crystal grow | Details: 1.8-2M AMMONIUM FORMATE 100MM HEPES, PH 7.5 5MM MNCL2 10-15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2009 / Details: KB-MIRRORS |
Radiation | Monochromator: SI (111) CHANNEL-CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→49.23 Å / Num. obs: 78830 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 32.52 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.06→2.17 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 71 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X74 Resolution: 2.06→44.62 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.607 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.994 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→44.62 Å
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Refine LS restraints |
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