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Open data
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Basic information
Entry | Database: PDB / ID: 3m55 | ||||||
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Title | SET7/9 Y305F in complex with TAF10-K189me1 peptide and AdoHcy | ||||||
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Function / homology | ![]() SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / transcription factor TFTC complex / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / hepatocyte differentiation / protein-lysine N-methyltransferase activity ...SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / transcription factor TFTC complex / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / hepatocyte differentiation / protein-lysine N-methyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Del Rizzo, P.A. / Couture, J.-F. / Roiko, M.S. / Strunk, B.S. / Brunzelle, J.S. / Dirk, L.M. / Houtz, R.L. / Trievel, R.C. | ||||||
![]() | ![]() Title: SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation. Authors: Del Rizzo, P.A. / Couture, J.F. / Dirk, L.M. / Strunk, B.S. / Roiko, M.S. / Brunzelle, J.S. / Houtz, R.L. / Trievel, R.C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76 KB | Display | ![]() |
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PDB format | ![]() | 53.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3m53C ![]() 3m54C ![]() 3m56C ![]() 3m57C ![]() 3m58C ![]() 3m59C ![]() 3m5aC ![]() 2f69S 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: 29027.334 Da / Num. of mol.: 1 / Fragment: UNP residues 110-366 / Mutation: Y305F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8WTS6, ![]() |
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#2: Protein/peptide | Mass: 1268.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-SAH / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.32 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.95 M Sodium Citrate, 0.1 M Imidazole pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2008 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→30 Å / Num. obs: 56257 / % possible obs: 99.1 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.053 / Χ2: 1.092 / Net I/σ(I): 15.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2F69 Resolution: 1.55→29.19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.868 / SU B: 1.227 / SU ML: 0.045 / SU R Cruickshank DPI: 0.07 / SU Rfree: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.91 Å2 / Biso mean: 25.626 Å2 / Biso min: 9.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→29.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.586 Å / Total num. of bins used: 20
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