[English] 日本語
Yorodumi- PDB-5ph6: PanDDA analysis group deposition -- Crystal Structure of JMJD2D i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ph6 | ||||||
---|---|---|---|---|---|---|---|
Title | PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09736a | ||||||
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 / regulation of protein phosphorylation / double-strand break repair via homologous recombination ...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 / regulation of protein phosphorylation / double-strand break repair via homologous recombination / 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: 1.742 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ph6.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ph6.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ph6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/5ph6 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/5ph6 | HTTPS FTP |
---|
-Group deposition
ID | G_1002020 (24 entries) |
---|---|
Title | PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) |
Type | changed 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 |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 |
---|
-Non-polymers , 7 types, 396 molecules
#2: Chemical | ChemComp-ZN / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-NI / | ||||||
#4: Chemical | ChemComp-OGA / | ||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | yes c1ccc2c(c1)C(C(N2)=O)=O None -14 -16 -16 c1ccc2c(c1)C(C(N2)=O)=O 4 - High Confidence None 0. ... |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.64 % / Mosaicity: 0.05 ° |
---|---|
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 | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 1.74→29.316 Å / Num. obs: 40370 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 16.71 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.039 / Rrim(I) all: 0.141 / Net I/σ(I): 13.5 / Num. measured all: 523536 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4D6R Resolution: 1.742→29.316 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.49 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.5 Å2 / Biso mean: 20.1731 Å2 / Biso min: 6.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.742→29.316 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|