[English] 日本語
Yorodumi- PDB-5fxw: Crystal structure of JmjC domain of human histone demethylase UTY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fxw | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of JmjC domain of human histone demethylase UTY in complex with fumarate | ||||||||||||
Components | HISTONE DEMETHYLASE UTY | ||||||||||||
Keywords | TRANSFERASE / TCA INTERMEDIATE | ||||||||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone demethylase activity / HDMs demethylate histones / chromatin DNA binding / heart development / regulation of gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleoplasm / metal ion binding Similarity search - Function | ||||||||||||
Biological species | HOMO SAPIENS (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||||||||
Authors | Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||||||||
Citation | Journal: To be Published Title: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with Fumarate Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fxw.cif.gz | 206.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fxw.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fxw_validation.pdf.gz | 465 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fxw_full_validation.pdf.gz | 470.1 KB | Display | |
Data in XML | 5fxw_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 5fxw_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxw ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxw | HTTPS FTP |
-Related structure data
Related structure data | 3zliS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55006.402 Da / Num. of mol.: 2 / Fragment: JMJC DOMAIN, RESIDUES 878-1347 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O14607 |
---|
-Non-polymers , 5 types, 608 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.49 % / Description: NONE |
---|---|
Crystal grow | pH: 7.8 Details: 0.1M HEPES PH 7.8 -- 0.25M TRIMETHYLAMINE N-OXIDE -- 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→54.72 Å / Num. obs: 69482 / % possible obs: 98.9 % / Observed criterion σ(I): 1.2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.09→2.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZLI Resolution: 2.09→54.72 Å / σ(F): 1.34 / Stereochemistry target values: ML / Details: DISORDERED SIDE CHAINS WERE REMOVED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→54.72 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|