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Yorodumi- PDB-5pho: PanDDA analysis group deposition -- Crystal Structure of JMJD2D a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5pho | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 1) | ||||||
Components | Lysine-specific demethylase 4D | ||||||
Keywords | OXIDOREDUCTASE / PanDDA / SGC - Diamond I04-1 fragment screening / Jmj domain / epigenetics | ||||||
Function / homology | Function and homology information positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.4 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. / Vollmar, M. / Ng, J. / Szykowska, A. / Burgess-Brown, N. / Brennan, P.E. / Cox, O. / Oppermann, U. / 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 | 5pho.cif.gz | 103.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5pho.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 5pho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/5pho ftp://data.pdbj.org/pub/pdb/validation_reports/ph/5pho | HTTPS FTP |
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-Group deposition
ID | G_1002021 (224 entries) |
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Title | PanDDA analysis group deposition of models of ground state datasets |
Type | ground state |
Description | Jmjc domain of human JMJD2D screened against the ZENOBIA Fragment Library by X-ray Crystallography. Check out the PanDDA event maps at https://zenodo.org/record/290220/files/0_index.html |
-Related structure data
Related structure data | 4d6rS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42050.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Production host: Escherichia coli (E. coli) References: UniProt: Q6B0I6, 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 |
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-Non-polymers , 7 types, 456 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-NI / | ||||
#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | ChemComp-OGA / | ||||
#6: Chemical | ChemComp-EDO / #7: Chemical | #8: 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: 2.31 Å3/Da / Density % sol: 46.84 % / Mosaicity: 0.07 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 28% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.25M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2012 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→29.55 Å / Num. obs: 78705 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Net I/σ(I): 22.1 / Num. measured all: 978968 / 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: 4D6R Resolution: 1.4→29.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.925 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.81 Å2 / Biso mean: 16.719 Å2 / Biso min: 6.84 Å2
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Refinement step | Cycle: final / Resolution: 1.4→29.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.399→1.435 Å / Total num. of bins used: 20
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