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Yorodumi- PDB-5fhf: Crystal structure of Bacteroides sp Pif1 in complex with ADP-AlF4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fhf | ||||||
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Title | Crystal structure of Bacteroides sp Pif1 in complex with ADP-AlF4 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / Pif1 helicase / DNA helicase | ||||||
Function / homology | Function and homology information DNA helicase activity / telomere maintenance / nucleotide binding / DNA repair Similarity search - Function | ||||||
Biological species | Bacteroides sp. 2_1_16 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å | ||||||
Authors | Zhou, X. / Ren, W. / Bharath, S.R. / Song, H. | ||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1 Authors: Zhou, X. / Ren, W. / Bharath, S.R. / Tang, X. / He, Y. / Chen, C. / Liu, Z. / Li, D. / Song, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fhf.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fhf.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/5fhf ftp://data.pdbj.org/pub/pdb/validation_reports/fh/5fhf | HTTPS FTP |
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-Related 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: 49716.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides sp. 2_1_16 (bacteria) / Gene: HMPREF0101_01022 / Production host: Escherichia coli (E. coli) / References: UniProt: D1JM21, UniProt: A0A7U8QDR9*PLUS |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-ALF / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 200 mM MgCl2, 0.1 M Tris, 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→62.4 Å / Num. obs: 33204 / % possible obs: 98.9 % / Redundancy: 7.5 % / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.9 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Resolution: 2.15→44.78 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.52 / 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: 2.15→44.78 Å
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Refine LS restraints |
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LS refinement shell |
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