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- PDB-3oym: Crystal structure of the PFV N224H mutant intasome bound to manganese -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oym | ||||||
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Title | Crystal structure of the PFV N224H mutant intasome bound to manganese | ||||||
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![]() | RECOMBINATION / VIRAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / TETRAMER / DNA INTEGRATION / ENDONUCLEASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / NUCLEOTIDYLTRANSFERASE / NUCLEUS / TRANSFERASE / VIRAL NUCLEOPROTEIN / VIRION / DNA-BINDING / ZINC BINDING / HHCC MOTIF / VIRAL PROTEIN / INHIBITOR / DNA-BINDING PROTEIN-DNA complex / VIRAL PROTEIN-DNA complex | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Hare, S. / Cherepanov, P. | ||||||
![]() | ![]() Title: Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance. Authors: Hare, S. / Vos, A.M. / Clayton, R.F. / Thuring, J.W. / Cummings, M.D. / Cherepanov, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.5 KB | Display | ![]() |
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PDB format | ![]() | 123.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494.7 KB | Display | ![]() |
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Full document | ![]() | 503.2 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 45.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3oyaC ![]() 3oybC ![]() 3oycC ![]() 3oydC ![]() 3oyeC ![]() 3oyfC ![]() 3oygC ![]() 3oyhC ![]() 3oyiC ![]() 3oyjC ![]() 3oykC ![]() 3oylC ![]() 3oynC ![]() 3oy9S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44480.738 Da / Num. of mol.: 2 / Fragment: UNP residues 752 to 1143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Donor DNA non-transferred strand |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Donor DNA transferred strand |
-Non-polymers , 7 types, 610 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / | ||||||||||
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#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-NH4 / | #9: Chemical | ChemComp-HEZ / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.02→39.894 Å / Num. obs: 99967 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.106 / Net I/σ(I): 8.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3OY9 Resolution: 2.02→39.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2317 / WRfactor Rwork: 0.1995 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8528 / SU B: 3.292 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1159 / SU Rfree: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 98.81 Å2 / Biso mean: 37.6561 Å2 / Biso min: 18.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→39.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.072 Å / Total num. of bins used: 20
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