+Open data
-Basic information
Entry | Database: PDB / ID: 4zo0 | ||||||
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Title | X-ray Structure of AAV-2 Origin Binding Domain | ||||||
Components | Protein Rep68 | ||||||
Keywords | HYDROLASE / DNA binding protein / Adeno-Associated Virus / HUH nuclease | ||||||
Function / homology | Function and homology information symbiont-mediated arrest of host cell cycle during G2/M transition / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / viral DNA genome replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endonuclease activity / DNA replication / DNA helicase / host cell nucleus / ATP hydrolysis activity ...symbiont-mediated arrest of host cell cycle during G2/M transition / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / viral DNA genome replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endonuclease activity / DNA replication / DNA helicase / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Adeno-associated virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Musayev, F.N. / Zarate-Perez, F. / Escalante, C.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2015 Title: Structural Studies of AAV2 Rep68 Reveal a Partially Structured Linker and Compact Domain Conformation. Authors: Musayev, F.N. / Zarate-Perez, F. / Bardelli, M. / Bishop, C. / Saniev, E.F. / Linden, R.M. / Henckaerts, E. / Escalante, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zo0.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zo0.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zo0_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 4zo0_full_validation.pdf.gz | 478.1 KB | Display | |
Data in XML | 4zo0_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 4zo0_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/4zo0 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/4zo0 | HTTPS FTP |
-Related structure data
Related structure data | 5dcxC 1m55S 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24186.441 Da / Num. of mol.: 3 / Fragment: Origin Binding Domain (UNP residues 1-206) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Adeno-associated virus 2 (isolate Srivastava/1982) Strain: isolate Srivastava/1982 / Gene: Rep68 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P03132, DNA helicase #2: Chemical | ChemComp-IPA / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.89 Å3/Da / Density % sol: 68.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Isopropanol, Sodium acetate, Magnesium acetate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 50960 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 8.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M55 Resolution: 2.3→29.724 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.724 Å
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Refine LS restraints |
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LS refinement shell |
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