[English] 日本語
Yorodumi- PDB-5ztz: Proteobacterial origin of protein arginine methylation and regula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ztz | ||||||
---|---|---|---|---|---|---|---|
Title | Proteobacterial origin of protein arginine methylation and regulation of Complex I assembly by MidA | ||||||
Components | Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial | ||||||
Keywords | TRANSFERASE / Mitochondria Complex I / Methyl Transferase / MidA/NDUFAF7 / SAM / SAH / NDUFS2 | ||||||
Function / homology | Function and homology information Complex I biogenesis / pinocytosis / phototaxis / culmination involved in sorocarp development / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / glutamate metabolic process / thermotaxis / glycogen metabolic process / sporulation resulting in formation of a cellular spore ...Complex I biogenesis / pinocytosis / phototaxis / culmination involved in sorocarp development / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / glutamate metabolic process / thermotaxis / glycogen metabolic process / sporulation resulting in formation of a cellular spore / positive regulation of mitochondrial fission / mitochondrial respiratory chain complex I assembly / phagocytosis / ATP metabolic process / negative regulation of autophagy / methylation / mitochondrion Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Arold, S.T. / Swaminathan, K. / Hameed, U.F.S. | ||||||
Funding support | Singapore, 1items
| ||||||
Citation | Journal: Cell Rep / Year: 2018 Title: Proteobacterial Origin of Protein Arginine Methylation and Regulation of Complex I Assembly by MidA. Authors: Shahul Hameed, U.F.S. / Sanislav, O. / Lay, S.T. / Annesley, S.J. / Jobichen, C. / Fisher, P.R. / Swaminathan, K. / Arold, S.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ztz.cif.gz | 479.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ztz.ent.gz | 412.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ztz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ztz_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ztz_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 5ztz_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 5ztz_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/5ztz ftp://data.pdbj.org/pub/pdb/validation_reports/zt/5ztz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
#1: Protein | Mass: 47445.855 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: midA, DDB_G0282615 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q54S83, type II protein arginine methyltransferase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.33 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 8% ethylene glycol, 0.1M HEPES pH 7.5, 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 173 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9794, 0.9796, 0.9642 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2012 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.8→100.53 Å / Num. obs: 37830 / % possible obs: 96.81 % / Redundancy: 10.8 % / Rsym value: 0.17 / Net I/σ(I): 6.98 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 3505 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.8→100.53 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.899 / SU B: 30.679 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.281 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→100.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|