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Yorodumi- PDB-7owb: Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7owb | ||||||
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Title | Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-hydroxylase CalMB | ||||||
Components | Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Carminomycin-4-O-methyltransferase variant / Chimeragenesis / aclacinomycin 10-hydroxylase | ||||||
Function / homology | Function and homology information carminomycin 4-O-methyltransferase / daunorubicin biosynthetic process / O-methyltransferase activity / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Streptomyces peucetius (bacteria) Streptomyces sp. ZEA17I (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Dinis, P. / MetsaKetela, M. | ||||||
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 | 7owb.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7owb.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 7owb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7owb_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7owb_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7owb_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 7owb_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7owb ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7owb | HTTPS FTP |
-Related structure data
Related structure data | 7oy1C 7pg7C 7pgaC 7pgjC 7phdC 7pheC 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: 40304.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces peucetius (bacteria), (gene. exp.) Streptomyces sp. ZEA17I (bacteria) Gene: dnrK, DKT74_09280 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 References: UniProt: Q06528, UniProt: A0A2V2Q0Q4, carminomycin 4-O-methyltransferase |
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#2: Chemical | ChemComp-3VL / |
#3: Chemical | ChemComp-SAH / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryocooling / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 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: 2.45→44.87 Å / Num. obs: 15812 / % possible obs: 99.13 % / Redundancy: 5.69 % / Biso Wilson estimate: 51.87 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.19 |
Reflection shell | Resolution: 2.45→2.59 Å / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 5507 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TW2 Resolution: 2.45→44.87 Å / SU ML: 0.4449 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1495 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: 47.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→44.87 Å
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Refine LS restraints |
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LS refinement shell |
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