[English] 日本語
Yorodumi- PDB-5fy0: Crystal structure of JmjC domain of human histone demethylase UTY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fy0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of JmjC domain of human histone demethylase UTY in complex with L-malate | ||||||
Components | HISTONE DEMETHYLASE UTY | ||||||
Keywords | TRANSFERASE / TRASNFERASE / 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 / 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: 2.14 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 L-Malate 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 | 5fy0.cif.gz | 205.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fy0.ent.gz | 162.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fy0_validation.pdf.gz | 466.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fy0_full_validation.pdf.gz | 471.2 KB | Display | |
Data in XML | 5fy0_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 5fy0_validation.cif.gz | 57.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/5fy0 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/5fy0 | 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, 615 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.31 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: 0.1M BIS-TRIS PH 6.5 -- 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→70.59 Å / Num. obs: 68161 / % possible obs: 99.7 % / Observed criterion σ(I): 1.1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZLI Resolution: 2.14→70.587 Å / σ(F): 1.34 / Stereochemistry target values: ML / Details: DISORDERED SIDE CHAINS WERE REMOVED.
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→70.587 Å
|