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Yorodumi- PDB-5kch: SETDB1 in complex with an early stage, low affinity fragment cand... -
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-Basic information
Entry | Database: PDB / ID: 5kch | |||||||||
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Title | SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into weak electron density | |||||||||
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: 1.7 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 | 5kch.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kch.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kch_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
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Full document | 5kch_full_validation.pdf.gz | 468.1 KB | Display | |
Data in XML | 5kch_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5kch_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/5kch ftp://data.pdbj.org/pub/pdb/validation_reports/kc/5kch | HTTPS FTP |
-Related structure data
Related structure data | 5kcoSC S: Starting model for refinement C: citing same article (ref.) |
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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, 169 molecules
#2: Chemical | ChemComp-UNX / #3: Chemical | ChemComp-DMS / | #4: Chemical | #5: Chemical | ChemComp-6RN / | #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: 48.35 % |
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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: 1.7→43.82 Å / Num. obs: 28318 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.54 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Net I/σ(I): 10.5 / Num. measured all: 176868 | ||||||||||||||||||||||||||||||
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: 5KCO Resolution: 1.7→43.82 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.75 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 and modified by removal of plane restraints for atoms {C11, C4, N, C5} and atoms {N, C4, C5, H5}. The methyl group of the fragment candidate was not resolved by electron density and was omitted from the model. Ambiguous difference density suggests more than one main chain conformation for residues 235..239.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.71 Å2 / Biso mean: 25.14 Å2 / Biso min: 11.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→43.82 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 24.3406 Å / Origin y: 63.5815 Å / Origin z: 7.5794 Å
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Refinement TLS group | Selection details: chain A |