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Yorodumi- PDB-5kco: SETDB1 in complex with an early stage, low affinity fragment cand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kco | ||||||
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Title | SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy | ||||||
Components | Histone-lysine N-methyltransferase SETDB1 | ||||||
Keywords | TRANSFERASE / Fragment Screening / DIAMOND I04-1 XCHEM / PANDDA / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / 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 / 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 / Resolution: 1.47 Å | ||||||
Authors | Tempel, W. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Walker, J.R. / Brown, P.J. / Schapira, M. / Collins, P. / Pearce, N. / Brandao-Neto, J. ...Tempel, W. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Walker, J.R. / Brown, P.J. / Schapira, M. / Collins, P. / Pearce, N. / Brandao-Neto, J. / Douangamath, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Santhakumar, V. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy Authors: Tempel, W. / Harding, R.J. / Mader, P. / Dobrovetsky, E. / Walker, J.R. / Brown, P.J. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Santhakumar, S. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kco.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kco.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kco_validation.pdf.gz | 461.6 KB | Display | wwPDB validaton report |
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Full document | 5kco_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 5kco_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 5kco_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/5kco ftp://data.pdbj.org/pub/pdb/validation_reports/kc/5kco | HTTPS FTP |
-Related structure data
Related structure data | 5kchC 3dlmS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26337.348 Da / Num. of mol.: 1 / Fragment: UNP residues 196-403 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETDB1, KIAA0067, KMT1E / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus References: UniProt: Q15047, histone-lysine N-methyltransferase |
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-Non-polymers , 5 types, 196 molecules
#2: Chemical | #3: Chemical | ChemComp-6RO / ~{ | #4: Chemical | ChemComp-UNX / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 48.33 % / Mosaicity: 0.06 ° |
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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. Trypsin had been added to the protein stock solution. |
-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-F / 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: 1.47→47.3 Å / Num. obs: 43355 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Net I/σ(I): 11.8 / Num. measured all: 284319 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3DLM Resolution: 1.47→47.3 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.422 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Users of this crystal structure: verify our intepretion of the electron density. Amplitudes and unmerged intensities are included with this deposition. Diffraction images will be deposited ...Details: Users of this crystal structure: verify our intepretion of the electron density. Amplitudes and unmerged intensities are included with this deposition. Diffraction images will be deposited in a public repository. Geometry restraints for the fragment candidate were prepared with GRADE. Some occupancies were refined with PHENIX software. Ambiguous difference density suggests more than one main chain conformation for residues 235..239.
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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: 66.74 Å2 / Biso mean: 20.634 Å2 / Biso min: 10.36 Å2
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Refinement step | Cycle: final / Resolution: 1.47→47.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.508 Å / Total num. of bins used: 20
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