+Open data
-Basic information
Entry | Database: PDB / ID: 6g25 | ||||||
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Title | X-ray structure of NSD3-PWWP1 in complex with compound 4 | ||||||
Components | Histone-lysine N-methyltransferase NSD3 | ||||||
Keywords | ONCOPROTEIN / Inhibitor / PWWP domain | ||||||
Function / homology | Function and homology information [histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation ...[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.432 Å | ||||||
Authors | Boettcher, J. / Muellauer, B.J. / Weiss-Puxbaum, A. / Zoephel, A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2019 Title: Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Authors: Bottcher, J. / Dilworth, D. / Reiser, U. / Neumuller, R.A. / Schleicher, M. / Petronczki, M. / Zeeb, M. / Mischerikow, N. / Allali-Hassani, A. / Szewczyk, M.M. / Li, F. / Kennedy, S. / ...Authors: Bottcher, J. / Dilworth, D. / Reiser, U. / Neumuller, R.A. / Schleicher, M. / Petronczki, M. / Zeeb, M. / Mischerikow, N. / Allali-Hassani, A. / Szewczyk, M.M. / Li, F. / Kennedy, S. / Vedadi, M. / Barsyte-Lovejoy, D. / Brown, P.J. / Huber, K.V.M. / Rogers, C.M. / Wells, C.I. / Fedorov, O. / Rumpel, K. / Zoephel, A. / Mayer, M. / Wunberg, T. / Bose, D. / Zahn, S. / Arnhof, H. / Berger, H. / Reiser, C. / Hormann, A. / Krammer, T. / Corcokovic, M. / Sharps, B. / Winkler, S. / Haring, D. / Cockcroft, X.L. / Fuchs, J.E. / Mullauer, B. / Weiss-Puxbaum, A. / Gerstberger, T. / Boehmelt, G. / Vakoc, C.R. / Arrowsmith, C.H. / Pearson, M. / McConnell, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g25.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g25.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 6g25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g25_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 6g25_full_validation.pdf.gz | 437.5 KB | Display | |
Data in XML | 6g25_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 6g25_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/6g25 ftp://data.pdbj.org/pub/pdb/validation_reports/g2/6g25 | HTTPS FTP |
-Related structure data
Related structure data | 6g24C 6g27C 6g29C 6g2bC 6g2cC 6g2eC 6g2fC 6g2oC 6g3pC 6g3tC 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
#1: Protein | Mass: 16271.401 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NSD3, WHSC1L1, DC28 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BZ95, histone-lysine N-methyltransferase |
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#2: Chemical | ChemComp-EHQ / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.432→38.28 Å / Num. obs: 25595 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.054 / Rsym value: 0.049 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.432→1.437 Å / Redundancy: 6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7148 / CC1/2: 0.889 / Rpim(I) all: 0.229 / Rrim(I) all: 0.587 / Rsym value: 0.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.432→38.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.075 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.071
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Displacement parameters | Biso max: 131.26 Å2 / Biso mean: 33.69 Å2 / Biso min: 13.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.432→38.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.432→1.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: -8.0994 Å / Origin y: 9.6692 Å / Origin z: -12.268 Å
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Refinement TLS group | Selection details: { A|* } |