+Open data
-Basic information
Entry | Database: PDB / ID: 8xak | ||||||
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Title | Structure of Pif1-G4 complex | ||||||
Components |
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Keywords | HYDROLASE/DNA / Pif1 / HYDROLASE / HYDROLASE-DNA complex | ||||||
Function / homology | ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / : / DNA / DNA (> 10) / : Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Hong, Z. / Song, H. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge. Authors: Hong, Z. / Byrd, A.K. / Gao, J. / Das, P. / Tan, V.Q. / Malone, E.G. / Osei, B. / Marecki, J.C. / Protacio, R.U. / Wahls, W.P. / Raney, K.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 | 8xak.cif.gz | 466.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xak.ent.gz | 378.4 KB | Display | PDB format |
PDBx/mmJSON format | 8xak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xak_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 8xak_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 8xak_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 8xak_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/8xak ftp://data.pdbj.org/pub/pdb/validation_reports/xa/8xak | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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 ACDB
#1: Protein | Mass: 61691.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: PIF1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4BX49 #2: DNA chain | Mass: 10697.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 12 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-K / |
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-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: 3.39 Å3/Da / Density % sol: 63.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.9, 22.5 %(w/v) PEG 400, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→48 Å / Num. obs: 22444 / % possible obs: 99.35 % / Redundancy: 1.9 % / CC1/2: 0.904 / Net I/σ(I): 3.05 |
Reflection shell | Resolution: 3.5→3.625 Å / Num. unique obs: 2168 / CC1/2: 0.611 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→48 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.61 / 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: 3.5→48 Å
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Refine LS restraints |
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LS refinement shell |
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