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- PDB-6s3h: Crystal structure of helicase Pif1 from Thermus oshimai in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6s3h | ||||||
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Title | Crystal structure of helicase Pif1 from Thermus oshimai in complex with ADP-AlF4 and (dT)7ds11bp | ||||||
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![]() | HYDROLASE / DNA helicase | ||||||
Function / homology | ![]() DNA helicase activity / telomere maintenance / DNA repair / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 384.6 KB | Display | ![]() |
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PDB format | ![]() | 310.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6s3eC ![]() 6s3iC ![]() 6s3mC ![]() 6s3nC ![]() 6s3oC ![]() 6s3pC ![]() 6xztC ![]() 7adaC ![]() 7bilC ![]() 5ftdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / DNA chain , 2 types, 4 molecules ABDE
#1: Protein | Mass: 50440.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 2084.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 502 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Sodium Hepes-MOPS 0.1M CaCl2 0.03M MgCl2 0.03M PEG 8000 10% Ethylene glycol 20% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 2.057→53.86 Å / Num. obs: 66828 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 36.91 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.0682 / Rpim(I) all: 0.0338 / Rrim(I) all: 0.08108 / Net I/σ(I): 10.71 |
Reflection shell | Resolution: 2.057→2.131 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.3774 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 5458 / CC1/2: 0.848 / Rpim(I) all: 0.2785 / Rrim(I) all: 0.4722 / % possible all: 79.35 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FTD Resolution: 2.06→29.51 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.158
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Displacement parameters | Biso mean: 56.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→29.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.08 Å / Total num. of bins used: 50
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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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