+Open data
-Basic information
Entry | Database: PDB / ID: 2py5 | ||||||
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Title | Phi29 DNA polymerase complexed with single-stranded DNA | ||||||
Components |
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Keywords | REPLICATION / TRANSFERASE/DNA / protein-dna complex / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information nucleoside binding / viral DNA genome replication / exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Berman, A.J. / Kamtekar, S. / Goodman, J.L. / Lazaro, J.M. / de Vega, M. / Blanco, L. / Salas, M. / Steitz, T.A. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases Authors: Berman, A.J. / Kamtekar, S. / Goodman, J.L. / Lazaro, J.M. / de Vega, M. / Blanco, L. / Salas, M. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2py5.cif.gz | 294.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2py5.ent.gz | 229.8 KB | Display | PDB format |
PDBx/mmJSON format | 2py5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2py5_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
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Full document | 2py5_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | 2py5_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 2py5_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/2py5 ftp://data.pdbj.org/pub/pdb/validation_reports/py/2py5 | HTTPS FTP |
-Related structure data
Related structure data | 2pyjC 2pylC 2pzsC 1xhxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 2128.421 Da / Num. of mol.: 5 / Source method: obtained synthetically #2: Protein | Mass: 66720.914 Da / Num. of mol.: 2 / Mutation: D12A,D66A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Gene: 2, gp2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03680, DNA-directed DNA polymerase #3: Chemical | ChemComp-EDO / #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: 2.37 Å3/Da / Density % sol: 48.16 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 12% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2006 |
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.601→50 Å / Num. all: 176187 / Num. obs: 172311 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 49.9 |
Reflection shell | Resolution: 1.601→1.66 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: copy C of 1XHX without residues 359-394 Resolution: 1.6→40.59 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.97 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.563 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→40.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.601→1.643 Å / Total num. of bins used: 20
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