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Yorodumi- PDB-7phe: Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7phe | ||||||
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Title | Chimeric carminomycin-4-O-methyltransferase (DnrK) with regions from 10-hydroxylase RdmB and 10-decarboxylase TamK | ||||||
Components | Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein,Aclacinomycin 10-hydroxylase RdmB | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / tsukubarubicin 10-decarboxylase | ||||||
Function / homology | Function and homology information 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 | Streptomyces peucetius (bacteria) Streptomyces tsukubensis (bacteria) Streptomyces purpurascens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Dinis, P. / MetsaKetela, M. | ||||||
Funding support | 1items
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Citation | Journal: Pnas Nexus / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7phe.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7phe.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 7phe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7phe_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7phe_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7phe_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 7phe_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/7phe ftp://data.pdbj.org/pub/pdb/validation_reports/ph/7phe | HTTPS FTP |
-Related structure data
Related structure data | 7owbC 7oy1C 7pg7C 7pgaC 7pgjC 7phdC 7phfC 1tw2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39982.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces peucetius (bacteria), (gene. exp.) Streptomyces tsukubensis (strain DSM 42081 / NBRC 108919 / NRRL 18488 / 9993) (bacteria), (gene. exp.) Streptomyces purpurascens (bacteria) Gene: dnrK, STSU_011780, STSU_11775, rdmB / Strain: DSM 42081 / NBRC 108919 / NRRL 18488 / 9993 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 References: UniProt: Q06528, UniProt: I2N5E8, UniProt: Q54527, carminomycin 4-O-methyltransferase, Lyases; Carbon-carbon lyases; Carboxy-lyases #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M Magnesium chloride hexahydrate; 0.1 M HEPES 7.0; 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: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.316→55.713 Å / Num. obs: 33595 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 39.21 Å2 / Rpim(I) all: 0.124 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.316→2.356 Å / Num. unique obs: 1674 / Rpim(I) all: 0.537 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tw2 Resolution: 2.32→55.71 Å / SU ML: 0.3626 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.9121 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: 42.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→55.71 Å
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Refine LS restraints |
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LS refinement shell |
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