+Open data
-Basic information
Entry | Database: PDB / ID: 5gn1 | ||||||
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Title | Crystal structure of the C-terminal part of Fun30 ATPase domain | ||||||
Components | ATP-dependent helicase FUN30 | ||||||
Keywords | HYDROLASE / helicase / recA / remodeler | ||||||
Function / homology | Function and homology information : / : / : / subtelomeric heterochromatin formation => GO:0031509 / chromatin remodeling => GO:0006338 / mating-type region heterochromatin / ATP-dependent chromatin remodeler activity => GO:0140658 / DNA double-strand break processing / rDNA heterochromatin formation / silent mating-type cassette heterochromatin formation ...: / : / : / subtelomeric heterochromatin formation => GO:0031509 / chromatin remodeling => GO:0006338 / mating-type region heterochromatin / ATP-dependent chromatin remodeler activity => GO:0140658 / DNA double-strand break processing / rDNA heterochromatin formation / silent mating-type cassette heterochromatin formation / chromosome, centromeric region / ATP-dependent activity, acting on DNA / heterochromatin formation / DNA helicase activity / positive regulation of RNA splicing / DNA helicase / chromosome, telomeric region / chromatin remodeling / chromatin binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Jiang, T. / Liu, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2017 Title: Crystal structure of the ATPase-C domain of the chromatin remodeller Fun30 from Saccharomyces cerevisiae. Authors: Liu, L. / Jiang, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gn1.cif.gz | 291 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gn1.ent.gz | 232.8 KB | Display | PDB format |
PDBx/mmJSON format | 5gn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/5gn1 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/5gn1 | HTTPS FTP |
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-Related structure data
Related structure data | 3mwyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42406.977 Da / Num. of mol.: 4 / Fragment: UNP residues 780-1122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: FUN30 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P31380, DNA helicase #2: Water | ChemComp-HOH / | |
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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: 2.13 Å3/Da / Density % sol: 42.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Sodium malonate, 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 103556 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.88 Å2 / Net I/σ(I): 20.73 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.13 / CC1/2: 0.86 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mwy Resolution: 1.95→36.205 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.65 / 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: 1.95→36.205 Å
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Refine LS restraints |
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LS refinement shell |
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