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Open data
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Basic information
Entry | Database: PDB / ID: 6uwd | ||||||||||||
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Title | Crystal structure of Apo AtmM | ||||||||||||
![]() | D-glucose O-methyltransferase | ||||||||||||
![]() | TRANSFERASE / methyltransferase / natural products / indolocarbazole / SAM | ||||||||||||
Function / homology | ![]() S-adenosylmethionine-dependent methyltransferase activity / methylation / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Alvarado, S.K. / Wang, Z. / Miller, M.D. / Thorson, J.S. / Phillips Jr., G.N. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Apo AtmM Authors: Alvarado, S.K. / Miller, M.D. / Wang, Z. / Thorson, J.S. / Phillips Jr., G.N. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.8 KB | Display | ![]() |
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PDB format | ![]() | 123.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 261.9 KB | Display | ![]() |
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Full document | ![]() | 261.8 KB | Display | |
Data in XML | ![]() | 1.1 KB | Display | |
Data in CIF | ![]() | 3.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uvqC ![]() 3busS 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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1 |
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28669.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.42 Å3/Da / Density % sol: 72.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.20M Magnesium acetate, 16% PEG 3350 and 10% of ATP disodium salt, Benzidine, L-Carnitine hydrochloride, Sulfanilamide, Cytosine in 0.02M HEPES sodium pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 26, 2019 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03326 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→102.73 Å / Num. obs: 32348 / % possible obs: 99.6 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.019 / Rrim(I) all: 0.06 / Net I/σ(I): 17.8 / Num. measured all: 317358 / Scaling rejects: 256 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3bus Resolution: 2.04→59.31 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.89 Å2 / Biso mean: 68.3605 Å2 / Biso min: 39.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→59.31 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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