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Yorodumi- PDB-7k82: The X-ray crystal structure of SSR4, an S. pombe chromatin remode... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k82 | ||||||
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Title | The X-ray crystal structure of SSR4, an S. pombe chromatin remodelling protein: sulfur SAD | ||||||
Components | SWI/SNF and RSC complexes subunit ssr4 | ||||||
Keywords | GENE REGULATION / chromatin remodelling / SAD phasing / novel structure | ||||||
Function / homology | Function and homology information RSC-type complex / SWI/SNF complex / transcription initiation-coupled chromatin remodeling / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Peat, T.S. / Newman, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: The X-ray crystal structure of the N-terminal domain of Ssr4, a Schizosaccharomyces pombe chromatin-remodelling protein. Authors: Newman, J. / Nebl, T. / Van, H. / Peat, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k82.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k82.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 7k82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k82_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 7k82_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 7k82_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 7k82_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/7k82 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/7k82 | HTTPS FTP |
-Related structure data
Related structure data | 7k7vSC 7k7wC 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: 22334.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: ssr4, SPBP23A10.05 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P7Y0 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.82 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: Crystallisation experiments were set up in SD2 sitting drop plates at 8 C with 200 nL protein plus 200 nL reservoir with 50 uL of reservoir in the wells. The protein concentration was 5 ...Details: Crystallisation experiments were set up in SD2 sitting drop plates at 8 C with 200 nL protein plus 200 nL reservoir with 50 uL of reservoir in the wells. The protein concentration was 5 mg/mL. Reservoir conditions contained 1.5 to 1.9 M ammonium sulfate, 0.7-12% dioxane and either 100 mM MES, 100 mM bis-tris or 10% (v/v) malate-MES-tris buffer at a pH between 5.5 and 5.8 PH range: 5.5 - 5.8 |
-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: 1.5486 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5486 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.4 Å / Num. obs: 14204 / % possible obs: 99.9 % / Redundancy: 97.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.355 / Rpim(I) all: 0.036 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 101 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1128 / CC1/2: 0.753 / Rpim(I) all: 0.469 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7k7v Resolution: 2.1→40.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.581 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / ESU R: 0.194 / ESU R Free: 0.163 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.082 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40.4 Å
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Refine LS restraints |
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LS refinement shell |
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