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- PDB-8bvi: Crystal structure of the METTL9-like histidine methyltransferase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bvi | ||||||
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Title | Crystal structure of the METTL9-like histidine methyltransferase from Ostreococcus tauri | ||||||
![]() | DREV methyltransferase | ||||||
![]() | TRANSFERASE / methyltransferase / histidine methyltransferase / Rossmann fold | ||||||
Function / homology | protein-L-histidine N-pros-methyltransferase activity / Protein-L-histidine N-pros-methyltransferase / DREV methyltransferase / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DREV methyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hammerstad, M. / Schroer, L. / Hersleth, H.-P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: METTL9-like histidine methyltransferases Authors: Schroer, L. / Hammerstad, M. / Weirich, S. / Hersleth, H.-P. / Groensberg, I.A. / Hagen, L. / Slupphaug, G. / Davydova, E. / Falnes, P.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.5 KB | Display | ![]() |
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PDB format | ![]() | 103.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
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Full document | ![]() | 430.6 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 33902.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Methyltransferase-like protein 9 / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes pH 7.5, 0.2 M L-proline, 10% w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918402 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→75.59 Å / Num. obs: 7642 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 119.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.041 / Rrim(I) all: 0.124 / Χ2: 1 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1372 / CC1/2: 0.553 / Rpim(I) all: 0.648 / Rrim(I) all: 2.01 / Χ2: 1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 131.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→47.81 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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