+Open data
-Basic information
Entry | Database: PDB / ID: 7b07 | ||||||
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Title | TgoT_6G12 apo | ||||||
Components | DNA polymerase | ||||||
Keywords | DNA BINDING PROTEIN / archaea / polymerase | ||||||
Function / homology | Function and homology information nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Thermococcus gorgonarius (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å | ||||||
Authors | Samson, C. / Legrand, P. / Tekpinar, M. / Rozenski, J. / Abramov, M. / Holliger, P. / Pinheiro, V. / Herdewijn, P. / Delarue, M. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Biomolecules / Year: 2020 Title: Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution. Authors: Samson, C. / Legrand, P. / Tekpinar, M. / Rozenski, J. / Abramov, M. / Holliger, P. / Pinheiro, V.B. / Herdwijn, P. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b07.cif.gz | 320.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b07.ent.gz | 264.3 KB | Display | PDB format |
PDBx/mmJSON format | 7b07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b07_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 7b07_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 7b07_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 7b07_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b07 ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b07 | HTTPS FTP |
-Related structure data
Related structure data | 7b06C 7b08C 7b0fC 7b0gC 7b0hC 1tgoS 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
#1: Protein | Mass: 89884.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus gorgonarius (archaea) / Gene: pol, polA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P56689, DNA-directed DNA polymerase | ||
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#2: Chemical | ChemComp-CA / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 20K and 0.1 M MES-NaOH pH 6.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 3.099→49.53 Å / Num. obs: 132742 / % possible obs: 99.37 % / Redundancy: 3.4 % / Biso Wilson estimate: 106.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.193 / Net I/σ(I): 8.72 |
Reflection shell | Resolution: 3.099→3.21 Å / Rmerge(I) obs: 2.756 / Num. unique obs: 1621 / CC1/2: 0.552 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tgo Resolution: 3.099→49.53 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.868 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.487
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Displacement parameters | Biso max: 286.65 Å2 / Biso mean: 140.31 Å2 / Biso min: 85.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.099→49.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 42
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Refinement TLS params. | T11: 0.304 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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