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- PDB-5zzw: Proteobacterial origin of protein arginine methylation and regula... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zzw | ||||||
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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 | ![]() | 496.3 KB | Display | ![]() |
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PDB format | ![]() | 412.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 45.1 KB | Display | |
Data in CIF | ![]() | 60.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ztzSC ![]() 5zu0C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SAH / End label comp-ID: SAH / Refine code: _ / Auth seq-ID: 83 - 501 / Label seq-ID: 13
NCS ensembles :
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Components
#1: Protein | Mass: 46930.012 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: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M BIS-TRIS pH 6.5, 10% w/v polyethylene glycol 10000 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→54.54 Å / Num. obs: 43310 / % possible obs: 97.7 % / Redundancy: 6.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.186 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.59→2.693 Å / Num. unique obs: 4454 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZTZ Resolution: 2.6→54.54 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.901 / SU B: 42.695 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R: 0.963 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.264 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→54.54 Å
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Refine LS restraints |
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