+Open data
-Basic information
Entry | Database: PDB / ID: 8t3x | ||||||
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Title | TNA polymerase, closed ternary | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / transferase / transferase-DNA complex | ||||||
Function / homology | Function and homology information nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 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 | Thermococcus kodakarensis (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Maola, V. / Chaput, J. / Chim, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Directed Evolution of a Highly Efficient TNA Polymerase Achieved by Homologous Recombination Authors: Maola, V. / Yik, E. / Hajjar, M. / Lee, J. / Holguin, M. / Quijano, R. / Nguyen, K. / Ho, K. / Medina, J. / Chim, N. / Chaput, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t3x.cif.gz | 408.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t3x.ent.gz | 272.1 KB | Display | PDB format |
PDBx/mmJSON format | 8t3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t3x_validation.pdf.gz | 760 KB | Display | wwPDB validaton report |
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Full document | 8t3x_full_validation.pdf.gz | 770.4 KB | Display | |
Data in XML | 8t3x_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 8t3x_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/8t3x ftp://data.pdbj.org/pub/pdb/validation_reports/t3/8t3x | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 88459.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: engineered from Thermococcus kodakarensis DNA polymerase Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU9 |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 4585.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3633.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 50 molecules
#4: Chemical | ChemComp-9O7 / [( |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-EPE / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.18 Å3/Da / Density % sol: 43.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Lithium chloride , 0.1 M HEPES pH 6.5, 17.6% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→45.39 Å / Num. obs: 23008 / % possible obs: 99.03 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.32 Å2 / Rmerge(I) obs: 0.1773 / Net I/σ(I): 11.36 |
Reflection shell | Resolution: 2.73→2.828 Å / Rmerge(I) obs: 0.97 / Num. unique obs: 2237 / CC1/2: 0.766 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→45.39 Å / SU ML: 0.4171 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5518 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→45.39 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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