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Yorodumi- PDB-5qt2: PanDDA analysis group deposition -- Partial occupancy interpretat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5qt2 | ||||||
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Title | PanDDA analysis group deposition -- Partial occupancy interpretation of PanDDA event map: SETDB1 in complex with FMOPL000074a | ||||||
Components | Histone-lysine N-methyltransferase SETDB1 | ||||||
Keywords | TRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer | ||||||
Function / homology | Function and homology information [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / promoter-specific chromatin binding / PKMTs methylate histone lysines ...[histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / heterochromatin organization / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / promoter-specific chromatin binding / PKMTs methylate histone lysines / chromosome / methylation / negative regulation of gene expression / intracellular membrane-bounded organelle / chromatin binding / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.59 Å | ||||||
Authors | Harding, R.J. / Tempel, W. / DOUANGAMATH, A. / BRANDAO-NETO, J. / Collins, P.M. / Krojer, T. / Mader, P. / Schapira, M. / von Delft, F. / Bountra, C. ...Harding, R.J. / Tempel, W. / DOUANGAMATH, A. / BRANDAO-NETO, J. / Collins, P.M. / Krojer, T. / Mader, P. / Schapira, M. / von Delft, F. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Santhakumar, V. | ||||||
Citation | Journal: To Be Published Title: PanDDA analysis group deposition Authors: Harding, R.J. / Tempel, W. / DOUANGAMATH, A. / BRANDAO-NETO, J. / Collins, P.M. / Krojer, T. / Mader, P. / Schapira, M. / von Delft, F. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Santhakumar, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qt2.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qt2.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 5qt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/5qt2 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/5qt2 | HTTPS FTP |
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-Group deposition
ID | G_1002089 (2 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | XDomainX of XOrganismX None screened against the XXX Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 3dlmS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m3.irrmc.3953 / Data set type: diffraction image data |
Experimental dataset #2 | Data reference: 10.18430/m3.irrmc.c.1 / Data set type: diffraction image data |
Experimental dataset #3 | Data reference: 10.18430/m3.irrmc.4136 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26337.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, ESET, KIAA0067, KMT1E / Production host: Escherichia coli (E. coli) References: UniProt: Q15047, histone-lysine N-methyltransferase |
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-Non-polymers , 6 types, 144 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Chemical | #5: Chemical | ChemComp-UNX / #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.38 Å3/Da / Density % sol: 48.37 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG-3350, 0.2M lithium sulfate, 0.1M Bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→47.36 Å / Num. obs: 34541 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 13 / Num. measured all: 226203 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3DLM Resolution: 1.59→47.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.189 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.093 / 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: 66.82 Å2 / Biso mean: 23.549 Å2 / Biso min: 13.1 Å2
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Refinement step | Cycle: final / Resolution: 1.59→47.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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