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- PDB-1jx4: Crystal Structure of a Y-family DNA Polymerase in a Ternary Compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jx4 | ||||||
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Title | Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide | ||||||
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![]() | TRANSFERASE/DNA / DNA polymerase / protein-DNA complex / Y-family / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ling, H. / Boudsocq, F. / Woodgate, R. / Yang, W. | ||||||
![]() | ![]() Title: Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Authors: Ling, H. / Boudsocq, F. / Woodgate, R. / Yang, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.5 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-DNA chain , 2 types, 2 molecules PT
#1: DNA chain | Mass: 4105.685 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 5353.465 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 40539.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 528 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADI.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-ADI / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.53 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% PEG 3350, 0.1 M Hepes (pH 7.0), 100 mM calcium acetate, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Jun 1, 2001 / Details: mirrors |
Radiation | Monochromator: Si crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9832 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 58391 / Num. obs: 57010 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 5.04 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.34 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2815 / Rsym value: 0.554 / % possible all: 98.4 |
Reflection | *PLUS Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.554 |
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Processing
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Refinement | Method to determine structure: ![]() Details: mlhl: maximum likelihood target using amplitudes and phase probability distribution
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Displacement parameters | Biso mean: 34.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å / Rfactor Rfree error: 0.007
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 500 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.9 Å2 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.373 / Rfactor Rwork: 0.366 |