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- PDB-5qt1: PanDDA analysis group deposition -- Partial occupancy interpretat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5qt1 | ||||||
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Title | PanDDA analysis group deposition -- Partial occupancy interpretation of PanDDA event map: SETDB1 in complex with FMOMB000017a | ||||||
![]() | Histone-lysine N-methyltransferase SETDB1 | ||||||
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Function / homology | ![]() [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 monomethyltransferase activity / positive regulation of DNA methylation-dependent heterochromatin formation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / heterochromatin organization / 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 / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / heterochromatin organization / promoter-specific chromatin binding / PKMTs methylate histone lysines / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.5 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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: ![]() |
Experimental dataset #2 | Data reference: ![]() |
Experimental dataset #3 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q15047, ![]() |
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-Non-polymers , 6 types, 146 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DSJ.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DSJ.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-EDO / | ![]() #4: Chemical | ChemComp-DSJ / | #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.79 % / 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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→43.82 Å / Num. obs: 35453 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Net I/σ(I): 14.4 / Num. measured all: 231870 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3DLM Resolution: 1.58→43.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.062 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.091 / 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: 72.7 Å2 / Biso mean: 23.455 Å2 / Biso min: 13.13 Å2
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Refinement step | Cycle: final / Resolution: 1.58→43.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.621 Å / Total num. of bins used: 20
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