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- PDB-5ztz: Proteobacterial origin of protein arginine methylation and regula... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ztz | ||||||
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Title | Proteobacterial origin of protein arginine methylation and regulation of Complex I assembly by MidA | ||||||
![]() | Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial | ||||||
![]() | TRANSFERASE / Mitochondria Complex I / Methyl Transferase / MidA/NDUFAF7 / SAM / SAH / NDUFS2 | ||||||
Function / homology | ![]() 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 / positive regulation of mitochondrial fission / glycogen metabolic process ...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 / positive regulation of mitochondrial fission / glycogen metabolic process / sporulation resulting in formation of a cellular spore / mitochondrial respiratory chain complex I assembly / phagocytosis / ATP metabolic process / negative regulation of autophagy / methylation / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arold, S.T. / Swaminathan, K. / Hameed, U.F.S. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 479.8 KB | Display | ![]() |
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PDB format | ![]() | 412.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.6 KB | Display | ![]() |
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Full document | ![]() | 461.8 KB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 55.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 47445.855 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q54S83, type II protein arginine methyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.33 % |
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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 | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
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 |
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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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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
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Refinement step | Cycle: 1 / Resolution: 2.8→100.53 Å
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Refine LS restraints |
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