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Yorodumi- PDB-5pyz: PanDDA analysis group deposition -- Crystal Structure of SP100 af... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5pyz | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 95) | ||||||
Components | Nuclear autoantigen Sp-100 | ||||||
Keywords | TRANSCRIPTION / PanDDA / SGC - Diamond I04-1 fragment screening / bromodomain / epigenetics / XChemExplorer | ||||||
Function / homology | Function and homology information regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / response to type II interferon ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / response to type II interferon / negative regulation of DNA binding / DNA damage response, signal transduction by p53 class mediator / retinoic acid receptor signaling pathway / regulation of angiogenesis / SUMOylation of DNA damage response and repair proteins / type II interferon-mediated signaling pathway / response to retinoic acid / telomere maintenance / nuclear periphery / response to cytokine / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / nuclear body / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / negative regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.59 Å | ||||||
Authors | Pearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. ...Pearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Renjie, Z. / Dias, A. / Ng, J. / Brennan, P.E. / Cox, O. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Authors: Pearce, N.M. / Krojer, T. / Bradley, A.R. / Collins, P. / Nowak, R.P. / Talon, R. / Marsden, B.D. / Kelm, S. / Shi, J. / Deane, C.M. / von Delft, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5pyz.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5pyz.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 5pyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/5pyz ftp://data.pdbj.org/pub/pdb/validation_reports/py/5pyz | HTTPS FTP |
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-Group deposition
ID | G_1002025 (114 entries) |
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Title | PanDDA analysis group deposition of models of ground state datasets |
Type | ground state |
Description | human SP100 screened against the Maybridge Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1. Check out the PanDDA event maps at https://zenodo.org/record/290201/files/0_index.html |
-Related structure data
Related structure data | 4ptbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21498.564 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SP100 / Production host: Escherichia coli (E. coli) / References: UniProt: P23497 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MES / | #4: Chemical | #5: 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: 2.77 Å3/Da / Density % sol: 55.54 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M MES pH 6.1 -- 20% PEG20K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→37.99 Å / Num. obs: 60652 / % possible obs: 95.8 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Net I/σ(I): 14.2 / Num. measured all: 211103 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4PTB Resolution: 1.59→37.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.151 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.095 / 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: 145.73 Å2 / Biso mean: 28.053 Å2 / Biso min: 11.13 Å2
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Refinement step | Cycle: final / Resolution: 1.59→37.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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