+Open data
-Basic information
Entry | Database: PDB / ID: 2x74 | ||||||
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Title | Human foamy virus integrase - catalytic core. | ||||||
Components | INTEGRASE | ||||||
Keywords | VIRAL PROTEIN / RETROVIRAL INTEGRASE / DNA-DIRECTED DNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / DNA INTEGRATION / ASPARTYL PROTEASE / DNA RECOMBINATION / TRANSFERASE / NUCLEASE / HYDROLASE | ||||||
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 / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / 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 | HUMAN SPUMARETROVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 Å | ||||||
Authors | Rety, S. / Delelis, O. / Rezabkova, L. / Dubanchet, B. / Legrand, P. / Silhan, J. / Lewit-Bentley, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x74.cif.gz | 224.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x74.ent.gz | 190.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x74 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x74 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22765.379 Da / Num. of mol.: 6 / Fragment: CATALYTIC CORE, RESIDUES 861-1060 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN SPUMARETROVIRUS / Strain: HSRV2 / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14350 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ILE 878 TO MSE ENGINEERED RESIDUE IN CHAIN A, ILE 978 TO MSE ...ENGINEERED | Sequence details | R180K IN CDNA, I127M, I227M, L253M FOR PHASING WITH SEMET | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 40.8 % / Description: THIS DATA SET WAS USED FOR REFINEMENT |
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Crystal grow | Details: 1.8-2M AMMONIUM FORMATE, 100MM HEPES PH 7.5, 10-15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 180 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.033, 0.979 | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 12, 2008 / Details: KB-MIRRORS | |||||||||
Radiation | Monochromator: SI (111) CHANNEL-CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.34→34.58 Å / Num. obs: 57496 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 51.072 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.1 | |||||||||
Reflection shell | Resolution: 2.34→2.46 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 95.4 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.34→34.58 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.57 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.286 / 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: 58.164 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→34.58 Å
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