+Open data
-Basic information
Entry | Database: PDB / ID: 1rys | |||||||||
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Title | REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / CPD DIMER / LESION BYPASS / POLYMERASE / TRANSFERASE-DNA COMPLEX | |||||||||
Function / homology | Function and homology information SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||
Authors | Ling, H. / Boudsocq, F. / Plosky, B. / Woodgate, R. / Yang, W. | |||||||||
Citation | Journal: Nature / Year: 2003 Title: Replication of a Cis-Syn Thymine Dimer at Atomic Resolution Authors: Ling, H. / Boudsocq, F. / Plosky, B. / Woodgate, R. / Yang, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rys.cif.gz | 204.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rys.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rys_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1rys_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1rys_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 1rys_validation.cif.gz | 59.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/1rys ftp://data.pdbj.org/pub/pdb/validation_reports/ry/1rys | HTTPS FTP |
-Related 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
-DNA chain , 2 types, 4 molecules CEDF
#1: DNA chain | Mass: 4080.671 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 5353.465 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 40257.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: DPO4 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase |
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-Non-polymers , 5 types, 744 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-EDO / | #7: Chemical | #8: 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: 2.82 Å3/Da / Density % sol: 56.01 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG3350, CA(AC)2, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2002 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.9 Å / Num. obs: 69785 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 19.9 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS Highest resolution: 2.03 Å / Lowest resolution: 2.06 Å / % possible obs: 95 % / Rmerge(I) obs: 0.492 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→19.9 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.03→19.9 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 19.9 Å / Rfactor Rwork: 0.222 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.01 |