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Yorodumi- PDB-2pzs: Phi29 DNA polymerase complexed with primer-template DNA (post-tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pzs | ||||||
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Title | Phi29 DNA polymerase complexed with primer-template DNA (post-translocation binary complex) | ||||||
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 / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / exonuclease activity / 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: 2.6 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 | 2pzs.cif.gz | 480.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pzs.ent.gz | 388.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/2pzs ftp://data.pdbj.org/pub/pdb/validation_reports/pz/2pzs | HTTPS FTP |
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-Related structure data
Related structure data | 2py5C 2pyjC 2pylC 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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3 |
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4 |
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Unit cell |
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Details | The biological assembly contains one molecule of polymerase bound to primer-template DNA. Each asymmetric unit contains two complete biological assemblies and two complexes in which most of the DNA is disordered. |
-Components
#1: DNA chain | Mass: 3019.991 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 5180.388 Da / Num. of mol.: 4 / Source method: obtained synthetically #3: Protein | Mass: 66720.914 Da / Num. of mol.: 4 / 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 #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: 2.73 Å3/Da / Density % sol: 54.97 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris-HCl, 20% PEG 10000, 200 mM magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2005 |
Radiation | Monochromator: double flat Si crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 97325 / Num. obs: 95762 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: copy c of 1XHX without residues 358-394 Resolution: 2.6→45.22 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.859 / SU B: 25.272 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.012 / ESU R Free: 0.358 / 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: 22.349 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→45.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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