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Yorodumi- PDB-5yth: Structure of large fragment of DNA Polymerase I from Thermus aqua... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yth | |||||||||
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Title | Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dG | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA / REPLICATION / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information nucleoside binding / 5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | |||||||||
Biological species | Thermus aquaticus (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | |||||||||
Authors | Zeng, H. / Mondal, M. / Song, R.Y. / Zhang, J. / Xia, B. / Gao, Y.Q. / Yi, C.Q. | |||||||||
Funding support | China, 2items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2019 Title: Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Authors: Zeng, H. / Mondal, M. / Song, R. / Zhang, J. / Xia, B. / Liu, M. / Zhu, C. / He, B. / Gao, Y.Q. / Yi, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yth.cif.gz | 269.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yth.ent.gz | 212.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/5yth ftp://data.pdbj.org/pub/pdb/validation_reports/yt/5yth | HTTPS FTP |
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-Related structure data
Related structure data | 5ytcC 5ytdC 5yteC 5ytfC 5ytgC 5z3nC 4dfkS 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60865.887 Da / Num. of mol.: 1 / Fragment: large fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3633.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4985.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 79 molecules
#4: Chemical | ChemComp-DGT / | ||||
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#5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow | Temperature: 293.15 K / Method: evaporation / pH: 7 Details: 0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→94.63 Å / Num. obs: 20264 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 18.76 |
Reflection shell | Resolution: 2.53→2.57 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DFK Resolution: 2.53→94.63 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.907 / SU B: 39.249 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R: 1.786 / ESU R Free: 0.35 / 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: 59.834 Å2
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Refinement step | Cycle: 1 / Resolution: 2.53→94.63 Å
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Refine LS restraints |
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