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- PDB-7phd: Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7phd | ||||||
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Title | Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-decarboxylase TamK | ||||||
![]() | Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein | ||||||
![]() | BIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / tsukubarubicin 10-decarboxylase | ||||||
Function / homology | ![]() carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / O-methyltransferase activity / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grocholski, T. / 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 | ![]() | 148.3 KB | Display | ![]() |
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PDB format | ![]() | 110.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7owbC ![]() 7oy1C ![]() 7pg7C ![]() 7pgaC ![]() 7pgjC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40144.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dnrK, STSU_011780, STSU_11775 / Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Production host: ![]() ![]() References: UniProt: Q06528, UniProt: I2N5E8, carminomycin 4-O-methyltransferase |
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-Non-polymers , 5 types, 345 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/3VL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/3VL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M Magnesium chloride hexahydrate; 0.1 M Tris-HCl, pH=8.0; 20 % w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryocooling / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→100 Å / Num. obs: 300031 / % possible obs: 98.1 % / Redundancy: 2.69 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.18 |
Reflection shell | Resolution: 1.53→1.57 Å / Rmerge(I) obs: 0.588 / Num. unique obs: 21078 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TW2 Resolution: 1.53→48.04 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.2026 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: 21.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→48.04 Å
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Refine LS restraints |
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LS refinement shell |
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