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- PDB-5ww0: Crystal structure of Set7, a novel histone methyltransferase in S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ww0 | |||||||||||||||
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Title | Crystal structure of Set7, a novel histone methyltransferase in Schizossacharomyces pombe | |||||||||||||||
![]() | SET domain-containing protein 7 | |||||||||||||||
![]() | TRANSCRIPTION / Histone / methytransferase / Schizosaccharomyces pombe SET7 / Epigenetic | |||||||||||||||
Function / homology | ![]() histone H3K37 methyltransferase activity / sporulation resulting in formation of a cellular spore / Transferases; Transferring one-carbon groups; Methyltransferases / chromatin organization / methylation / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Mevius, D.E.H.F. / Shen, Y. / Morishita, M. / Carrozzini, B. / Caliandro, R. / di Luccio, E. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Set7 Is a H3K37 Methyltransferase in Schizosaccharomyces pombe and Is Required for Proper Gametogenesis. Authors: Shen, Y. / Mevius, D.E.H.F. / Caliandro, R. / Carrozzini, B. / Roh, Y. / Kim, J. / Kim, S. / Ha, S.C. / Morishita, M. / di Luccio, E. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.1 KB | Display | ![]() |
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PDB format | ![]() | 51.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.3 KB | Display | ![]() |
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Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h6zC ![]() 3kmaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19597.812 Da / Num. of mol.: 2 / Fragment: UNP residues 1-145 Source method: isolated from a genetically manipulated source Details: Authors state that YPYDVPDYAAPG at the C-terminal are detection tags Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: set7, SPCC297.04c / Plasmid: pTYB12 / Production host: ![]() ![]() References: UniProt: Q9Y7Q6, histone-lysine N-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.11 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% ethylene glycol (cryoprotectant for 101)250mM Ammonium Sulfate, 14% PEG 3.350, 1(protein):1(buffer):0.4 ratio of 0.3M Glycyl-glycyl-glycine (~48mM final conc), Protein ...Details: 30% ethylene glycol (cryoprotectant for 101)250mM Ammonium Sulfate, 14% PEG 3.350, 1(protein):1(buffer):0.4 ratio of 0.3M Glycyl-glycyl-glycine (~48mM final conc), Protein concentration(4mg/mL), Protein buffer(10mM Tris pH 7.5) Temperature(13), Well volume(500ul), 5uL of HCL (12.1M) was added to the reservoir drop prior to drop setup Temp details: 13 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 16, 2016 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 19879 / % possible obs: 95 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.824 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KMA Resolution: 2.1→45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.811 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.185 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/ F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→45 Å
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Refine LS restraints |
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