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Yorodumi- PDB-6qpl: Crystal structure of Spindlin1 in complex with the inhibitor MS31 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qpl | ||||||
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Title | Crystal structure of Spindlin1 in complex with the inhibitor MS31 | ||||||
Components | Spindlin-1 | ||||||
Keywords | CELL CYCLE / Epigenetics / Tudor domain / Methyl-Lysine / methyl-Arginine | ||||||
Function / homology | Function and homology information gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Johansson, C. / Krojer, T. / Xiong, Y. / Jin, J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.C.T. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Discovery of a Potent and Selective Fragment-like Inhibitor of Methyllysine Reader Protein Spindlin 1 (SPIN1). Authors: Xiong, Y. / Greschik, H. / Johansson, C. / Seifert, L. / Bacher, J. / Park, K.S. / Babault, N. / Martini, M. / Fagan, V. / Li, F. / Chau, I. / Christott, T. / Dilworth, D. / Barsyte-Lovejoy, ...Authors: Xiong, Y. / Greschik, H. / Johansson, C. / Seifert, L. / Bacher, J. / Park, K.S. / Babault, N. / Martini, M. / Fagan, V. / Li, F. / Chau, I. / Christott, T. / Dilworth, D. / Barsyte-Lovejoy, D. / Vedadi, M. / Arrowsmith, C.H. / Brennan, P. / Fedorov, O. / Jung, M. / Farnie, G. / Liu, J. / Oppermann, U. / Schule, R. / Jin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qpl.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qpl.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 6qpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qpl_validation.pdf.gz | 789 KB | Display | wwPDB validaton report |
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Full document | 6qpl_full_validation.pdf.gz | 790.4 KB | Display | |
Data in XML | 6qpl_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 6qpl_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/6qpl ftp://data.pdbj.org/pub/pdb/validation_reports/qp/6qpl | HTTPS FTP |
-Related structure data
Related structure data | 6i8lS 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 B
#1: Protein | Mass: 25499.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y657 |
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-Non-polymers , 7 types, 116 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-JC5 / [ | #5: Chemical | ChemComp-GLY / | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-GOL / | #8: 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: 2.84 Å3/Da / Density % sol: 56.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 60% MPD and 0.1 M SPG buffer pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→43.59 Å / Num. obs: 39340 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 21.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.034 / Rrim(I) all: 0.122 / Net I/σ(I): 11.9 / Num. measured all: 500260 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I8L Resolution: 1.6→40.773 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.93 Å2 / Biso mean: 32.6444 Å2 / Biso min: 14.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→40.773 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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