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- PDB-1ig9: Structure of the Replicating Complex of a Pol Alpha Family DNA Po... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ig9 | ||||||
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Title | Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase | ||||||
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![]() | TRANSFERASE/DNA / DNA polymerase / catalytic complex / fidelity / two metal ion mechanism / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / 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 / DNA replication proofreading / 3'-5'-DNA exonuclease activity / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Franklin, M.C. / Wang, J. / Steitz, T.A. | ||||||
![]() | ![]() Title: Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase Authors: Franklin, M.C. / Wang, J. / Steitz, T.A. #1: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.7 KB | Display | ![]() |
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PDB format | ![]() | 174.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 807.3 KB | Display | ![]() |
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Full document | ![]() | 836.1 KB | Display | |
Data in XML | ![]() | 41.2 KB | Display | |
Data in CIF | ![]() | 58.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ih7C ![]() 1clqS 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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Unit cell |
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Details | Each monomer constitutes a functional assembly. |
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Components
-DNA chain , 2 types, 2 molecules TP
#1: DNA chain | Mass: 5550.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Substrate DNA, template strand |
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#2: DNA chain | Mass: 4240.768 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Substrate DNA, primer strand (dideoxy-terminated) |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 104655.141 Da / Num. of mol.: 1 / Mutation: Exonuclease-deficient (D222A/D327A) mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 361 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TTP.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-TTP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: PEG 350 monomethyl ether, calcium chloride, sodium cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop / Details: Wang, J., (1997) Cell (Cambridge,Mass.), 89, 1087. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 38733 / Num. obs: 38733 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.61 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1CLQ, with non-protein atoms removed Resolution: 2.6→29.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 297902.47 / 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.16 Å2 / ksol: 0.318 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.64 Å / Rfactor Rfree error: 0.03 / 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 σ(F): 0 / % reflection Rfree: 9.7 % / Rfactor all: 10 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 61.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.396 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.325 |