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Open data
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Basic information
Entry | Database: PDB / ID: 7pg7 | ||||||
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Title | 10-decarboxylase TamK from Streptomyces tsukubaensis | ||||||
![]() | Methyltransferase | ||||||
![]() | BIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / tsukubarubicin 10-decarboxylase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nji Wandi, B. / Dinis, P. / MetsaKetela, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Evolution-inspired engineering of anthracycline methyltransferases. Authors: Dinis, P. / Tirkkonen, H. / Wandi, B.N. / Siitonen, V. / Niemi, J. / Grocholski, T. / Metsa-Ketela, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 59.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 781.1 KB | Display | ![]() |
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Full document | ![]() | 782 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7owbC ![]() 7oy1C ![]() 7pgaC ![]() 7pgjC ![]() 7phdC ![]() 7pheC ![]() 7phfC ![]() 1tw2S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 39861.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.04M potassium phosphate monobasic, 16% PEG 8000, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryocoolin / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→56.1 Å / Num. obs: 65700 / % possible obs: 96.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.12 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.51→1.54 Å / Rmerge(I) obs: 0.693 / Num. unique obs: 2707 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TW2 Resolution: 1.51→28.04 Å / SU ML: 0.1646 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.1057 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 29.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→28.04 Å
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Refine LS restraints |
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LS refinement shell |
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