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Yorodumi- PDB-6s3i: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s3i | ||||||
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Title | Crystal structure of helicase Pif1 from Thermus oshimai in complex with ssDNA (dT)18 and ADP-MgF4 | ||||||
Components |
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Keywords | HYDROLASE / DNA helicase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus oshimai (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.455 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 | 6s3i.cif.gz | 184.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3i.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 6s3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3i ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3i | HTTPS FTP |
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-Related structure data
Related structure data | 6s3eC 6s3hC 6s3mC 6s3nC 6s3oC 6s3pC 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
-Protein / DNA chain , 2 types, 2 molecules AC
#1: Protein | Mass: 50440.816 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: 4213.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus oshimai (bacteria) |
-Non-polymers , 4 types, 18 molecules
#3: Chemical | ChemComp-ADP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-MF4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MES-imidazole 0.1M PEG 4000 8% Ethylene glycol 1.25% Glycerol 16% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 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: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.455→59.57 Å / Num. obs: 17618 / % possible obs: 9.31 % / Redundancy: 12.3 % / Biso Wilson estimate: 63.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08393 / Rpim(I) all: 0.02506 / Rrim(I) all: 0.08774 / Net I/σ(I): 19.04 |
Reflection shell | Resolution: 2.455→2.543 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.089 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 1836 / CC1/2: 0.794 / Rpim(I) all: 0.303 / Rrim(I) all: 1.131 / % possible all: 99.14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FTD Resolution: 2.455→59.57 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.455→59.57 Å
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Refine LS restraints |
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LS refinement shell |
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