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Yorodumi- PDB-5ftf: Crystal structure of Pif1 helicase from Bacteroides double mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ftf | |||||||||
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Title | Crystal structure of Pif1 helicase from Bacteroides double mutant L95C-I339C | |||||||||
Components | TPR DOMAIN PROTEIN | |||||||||
Keywords | HYDROLASE / SF1B / G QUADRUPLEX / SH3 DOMAIN / CONFORMATIONAL CHANGE / DISULPHIDE BRIDGE | |||||||||
Function / homology | Function and homology information DNA helicase activity / telomere maintenance / nucleotide binding / DNA repair / metal ion binding Similarity search - Function | |||||||||
Biological species | BACTEROIDES (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.412 Å | |||||||||
Authors | Chen, W.-F. / Dai, Y.-X. / Duan, X.-L. / Liu, N.-N. / Shi, W. / Li, M. / Dou, S.-X. / Li, N. / Dong, Y.-H. / Rety, S. / Xi, X.-G. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Crystal Structures of the Bspif1 Helicase Reveal that a Major Movement of the 2B SH3 Domain is Required for DNA Unwinding Authors: Chen, W.-F. / Dai, Y.-X. / Duan, X.-L. / Liu, N.-N. / Shi, W. / Li, N. / Li, M. / Dou, S.-X. / Dong, Y.-H. / 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 | 5ftf.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ftf.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ftf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/5ftf ftp://data.pdbj.org/pub/pdb/validation_reports/ft/5ftf | HTTPS FTP |
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-Related structure data
Related structure data | 5ftbSC 5ftcC 5ftdC 5fteC 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: 49710.938 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES (bacteria) / Strain: SP. 3_1_23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7K0H3, DNA helicase |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
Sequence details | NCBI REFERENCE SEQUENCE WP_008647876.1 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M BIS-TRIS PROPANE PH 6.5 0.1M CALCIUM ACETATE 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979142 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979142 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→60.87 Å / Num. obs: 19410 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 52.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.15 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.57 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FTB Resolution: 2.412→60.868 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 34.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.412→60.868 Å
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Refine LS restraints |
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LS refinement shell |
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