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- PDB-7pgj: Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pgj | ||||||
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Title | Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions from 10-decarboxylate TamK and 10-hydroxylase RdmB, together with a single point mutation F297G | ||||||
![]() | Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB | ||||||
![]() | BIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / aclacinomycin 10-hydroxylase / tsukubarubicin 10-decarboxylase | ||||||
Function / homology | ![]() carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / O-methyltransferase activity / antibiotic biosynthetic process / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 62.9 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 | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7owbC ![]() 7oy1C ![]() 7pg7C ![]() 7pgaC ![]() 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: 39910.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: dnrK, STSU_011780, STSU_11775, rdmB / Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Production host: ![]() ![]() References: UniProt: Q06528, UniProt: I2N5E8, UniProt: Q54527, carminomycin 4-O-methyltransferase, Lyases; Carbon-carbon lyases; Carboxy-lyases |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-ZBX / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: in 0.1 M Sodium acetate, pH 4.6; 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→62.5 Å / Num. obs: 22162 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.32 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.13→2.21 Å / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 13.4 / Num. unique obs: 2165 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1tw2 Resolution: 2.13→53.32 Å / SU ML: 0.1907 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.1634 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: 19.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→53.32 Å
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Refine LS restraints |
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LS refinement shell |
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