+Open data
-Basic information
Entry | Database: PDB / ID: 1ih7 | ||||||
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Title | High-Resolution Structure of Apo RB69 DNA Polymerase | ||||||
Components | DNA POLYMERASE | ||||||
Keywords | TRANSFERASE / DNA polymerase / fingers / palm / thumb | ||||||
Function / homology | Function and homology information bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage RB69 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / phase extension / Resolution: 2.21 Å | ||||||
Authors | Franklin, M.C. / Wang, J. / Steitz, T.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: Structure of the Replicating Complex of a Pol alpha Family DNA Polymerase Authors: Franklin, M.C. / Wang, J. / Steitz, T.A. #1: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Crystal Structure of a Pol alpha Family Replication DNA Polymerase from Bacteriophage RB69 Authors: Wang, J. / Sattar, A.K. / Wang, C.C. / Karam, J.D. / Konigsberg, W.H. / Steitz, T.A. #2: Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: Building a Replisome from Interacting Pieces: Sliding Clamp Complexed to a Peptide from DNA Polymerase and a Polymerase Editing Complex Authors: Shamoo, Y. / 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 | 1ih7.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ih7.ent.gz | 157.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ih7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ih7_validation.pdf.gz | 828.9 KB | Display | wwPDB validaton report |
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Full document | 1ih7_full_validation.pdf.gz | 848.7 KB | Display | |
Data in XML | 1ih7_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 1ih7_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ih7 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ih7 | HTTPS FTP |
-Related structure data
Related structure data | 1ig9C 1wajS 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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1 |
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Unit cell |
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Details | Each monomer constitutes a functional assembly. |
-Components
#1: Protein | Mass: 104743.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: gp43 / Plasmid: pRB.43 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase | ||||
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#2: Chemical | #3: Chemical | ChemComp-GMP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.57 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Sodium citrate, sodium/potassium tartrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6.25 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.913 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 1999 / Details: double crystal monochromator |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.913 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 88785 / Num. obs: 88785 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 3 / Num. unique all: 4352 / % possible all: 98.1 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Method to determine structure: phase extension Starting model: PDB entry 1WAJ, with all non-protein atoms removed Resolution: 2.21→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 533579.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: Engh and Huber, as implemented in CNS Details: This refinement extended the previous apo-RB69 polymerase structure to higher resolution.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.24 Å2 / ksol: 0.375 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.21→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.24 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 7.9 % / Rfactor all: 10 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 48.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.368 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.328 |