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Yorodumi- PDB-6s3p: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s3p | ||||||
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Title | Crystal structure of helicase Pif1 from Thermus oshimai in complex with (dT)18 | ||||||
Components |
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Keywords | HYDROLASE / DNA helicase | ||||||
Function / homology | Function and homology information telomere maintenance / DNA helicase activity / DNA repair / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus oshimai (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.926 Å | ||||||
Authors | Dai, Y.X. / Chen, W.F. / Teng, F.Y. / Liu, N.N. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition. Authors: Dai, Y.X. / Chen, W.F. / Liu, N.N. / Teng, F.Y. / Guo, H.L. / Hou, X.M. / Dou, S.X. / Rety, S. / Xi, X.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s3p.cif.gz | 208.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3p.ent.gz | 163.2 KB | Display | PDB format |
PDBx/mmJSON format | 6s3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s3p_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 6s3p_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 6s3p_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 6s3p_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3p ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3p | HTTPS FTP |
-Related structure data
Related structure data | 6s3eC 6s3hC 6s3iC 6s3mC 6s3nC 6s3oC 6xztC 7adaC 7bilC 5ftdS 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: 50339.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus oshimai (bacteria) / Gene: Theos_1468 / Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): C2566H / References: UniProt: K7RJ88 |
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#2: DNA chain | Mass: 5430.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria) |
#3: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris-HCl 0.1M NaF 0.03M NaI 0.03M NaBr 0.03M MES 0.03M PEG 4K 10% Glycerol 20% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.926→37.73 Å / Num. obs: 38861 / % possible obs: 88.12 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 32.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0557 / Rpim(I) all: 0.02295 / Rrim(I) all: 0.0603 / Net I/σ(I): 21.62 |
Reflection shell | Resolution: 1.926→1.995 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.4628 / Mean I/σ(I) obs: 4.01 / Num. unique obs: 2388 / CC1/2: 0.937 / Rpim(I) all: 0.2079 / Rrim(I) all: 0.5095 / % possible all: 55.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FTD Resolution: 1.926→37.73 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.926→37.73 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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