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Yorodumi- PDB-5ytc: Large fragment of DNA Polymerase I from Thermus aquaticus in a cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ytc | |||||||||
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Title | Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA / REPLICATION / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information nucleoside binding / hydrolase activity, acting on ester bonds / 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: 2.28 Å | |||||||||
Authors | Zeng, H. / Mondal, M. / Song, R.Y. / Zhang, J. / Xia, B. / 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 | 5ytc.cif.gz | 276.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ytc.ent.gz | 216.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ytc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ytc_validation.pdf.gz | 834.5 KB | Display | wwPDB validaton report |
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Full document | 5ytc_full_validation.pdf.gz | 842.2 KB | Display | |
Data in XML | 5ytc_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 5ytc_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/5ytc ftp://data.pdbj.org/pub/pdb/validation_reports/yt/5ytc | HTTPS FTP |
-Related structure data
Related structure data | 5ytdC 5yteC 5ytfC 5ytgC 5ythC 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: 3890.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 5000.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 265 molecules
#4: Chemical | ChemComp-DTP / | ||
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#5: Chemical | #6: 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: 2.22 Å3/Da / Density % sol: 44.66 % |
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Crystal grow | Temperature: 293.15 K / Method: evaporation / pH: 8.5 Details: 0.2 M Mg(HCOO)2, 0.1 M Tris HCl (pH 8.5), 18% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Apr 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→94.3 Å / Num. obs: 25784 / % possible obs: 98 % / Redundancy: 5.1 % / Net I/σ(I): 19.27 |
Reflection shell | Resolution: 2.28→2.32 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DFK Resolution: 2.28→94.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.207 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.272 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.653 Å2
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Refinement step | Cycle: 1 / Resolution: 2.28→94.3 Å
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Refine LS restraints |
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