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Yorodumi- PDB-3l2u: Crystal structure of the Prototype Foamy Virus (PFV) intasome in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l2u | ||||||
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Title | Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and GS9137 (Elvitegravir) | ||||||
Components |
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Keywords | RECOMBINATION/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / ZINC / DNA-BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / RECOMBINATION / RECOMBINATION-DNA complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / virion component / 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 / DNA integration / virion component / 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 / aspartic-type endopeptidase activity / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å | ||||||
Authors | Hare, S. / Gupta, S.S. / Cherepanov, P. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Retroviral intasome assembly and inhibition of DNA strand transfer Authors: Hare, S. / Gupta, S.S. / Valkov, E. / Engelman, A. / Cherepanov, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l2u.cif.gz | 231.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l2u.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 3l2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l2u_validation.pdf.gz | 919.5 KB | Display | wwPDB validaton report |
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Full document | 3l2u_full_validation.pdf.gz | 933.8 KB | Display | |
Data in XML | 3l2u_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 3l2u_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/3l2u ftp://data.pdbj.org/pub/pdb/validation_reports/l2/3l2u | HTTPS FTP |
-Related structure data
Related structure data | 3l2qC 3l2rC 3l2vC 3l2wC 3oy9C 3dlrS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44456.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human spumaretrovirus / Strain: HSRV2 / Gene: POL / Plasmid: pSSH6P-PFV-INFL / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: P14350 |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 5864.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 19 nucleotide preprocessed PFV donor DNA |
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#3: DNA chain | Mass: 5163.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 17 nucleotide preprocessed PFV donor DNA |
-Non-polymers , 5 types, 10 molecules
#4: Chemical | ChemComp-ZN / | ||||||
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#5: Chemical | #6: Chemical | ChemComp-NH4 / | #7: Chemical | ChemComp-ELV / | #8: Chemical | ChemComp-GOL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 68 % / Mosaicity: 0.51 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.35M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50mM Mes-NaOH, pH 6.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å |
Detector | Type: ADSC / Detector: AREA DETECTOR / Date: Oct 13, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→38.102 Å / Num. all: 27284 / Num. obs: 27284 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.092 |
Reflection shell | Resolution: 3.15→3.32 Å / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DLR Resolution: 3.15→36.44 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 1 / SU B: 28.781 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.559 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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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 max: 173.81 Å2 / Biso mean: 105.387 Å2 / Biso min: 50.29 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→36.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 860 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.15→3.231 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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