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- PDB-5raa: PanDDA analysis group deposition -- Crystal Structure of JMJD1B i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5raa | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM009990a | ||||||
![]() | Lysine-specific demethylase 3B | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / antioxidant activity / histone deacetylase complex / transcription coregulator activity / HDMs demethylate histones / chromatin DNA binding / chromatin / regulation of transcription by RNA polymerase II ...histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / antioxidant activity / histone deacetylase complex / transcription coregulator activity / HDMs demethylate histones / chromatin DNA binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Snee, M. / Nowak, R. / Johansson, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U. | ||||||
![]() | ![]() Title: PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library Authors: Snee, M. / Nowak, R. / Johansson, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.3 KB | Display | ![]() |
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PDB format | ![]() | 132.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Group deposition
ID | G_1002146 (33 entries) |
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Title | PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library |
Type | changed state |
Description | Jmjc Domain of Human JMJD1B screened against the DSPL Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | ![]() 6rbjS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43075.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7LBC6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | ChemComp-S3Y / [( | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M bis-tris pH 5.5 21% PEG3350 0.3M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 30, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.57→89 Å / Num. obs: 129720 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Rrim(I) all: 0.057 / Net I/σ(I): 12.6 / Num. measured all: 442845 / Scaling rejects: 0 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.5 %
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6RBJ Resolution: 1.57→89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.382 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.078 / 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: 128.07 Å2 / Biso mean: 32.289 Å2 / Biso min: 13.2 Å2
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Refinement step | Cycle: final / Resolution: 1.57→89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.611 Å / Total num. of bins used: 20
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