+Open data
-Basic information
Entry | Database: PDB / ID: 5ftd | |||||||||
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Title | Crystal structure of Pif1 helicase from Bacteroides apo form | |||||||||
Components | TPR DOMAIN PROTEIN | |||||||||
Keywords | HYDROLASE / SF1B / G QUADRUPLEX / SH3 DOMAIN / CONFORMATIONAL CHANGE | |||||||||
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: 1.695 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 | 5ftd.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ftd.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 5ftd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/5ftd ftp://data.pdbj.org/pub/pdb/validation_reports/ft/5ftd | HTTPS FTP |
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-Related structure data
Related structure data | 5ftbSC 5ftcC 5fteC 5ftfC 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: 49730.969 Da / Num. of mol.: 1 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-PO4 / |
#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 0.1 CALCIUM ACETATE 10% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97539 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97539 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.56 Å / Num. obs: 48257 / % possible obs: 87 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 21.69 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.22 / % possible all: 46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FTB Resolution: 1.695→48.564 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 22.55 / 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: 1.695→48.564 Å
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Refine LS restraints |
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LS refinement shell |
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