+Open data
-Basic information
Entry | Database: PDB / ID: 8g5s | ||||||
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Title | Crystal structure of apo TnmJ | ||||||
Components | TnmJ | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Enediyne / Tiancimycin / Biosynthesis / Natural Product | ||||||
Function / homology | Methyltransferase domain / Methyltransferase domain / methyltransferase activity / methylation / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Putative methyltransferase Function and homology information | ||||||
Biological species | Streptomyces sp. CB03234 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Liu, Y.-C. / Li, G. / Gui, C. / Shen, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2024 Title: Cofactorless oxygenases guide anthraquinone-fused enediyne biosynthesis. Authors: Gui, C. / Kalkreuter, E. / Liu, Y.C. / Li, G. / Steele, A.D. / Yang, D. / Chang, C. / Shen, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g5s.cif.gz | 273.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g5s.ent.gz | 220.1 KB | Display | PDB format |
PDBx/mmJSON format | 8g5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/8g5s ftp://data.pdbj.org/pub/pdb/validation_reports/g5/8g5s | HTTPS FTP |
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-Related structure data
Related structure data | 8g5tC 8g5uC 5f8cS 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: 40704.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. CB03234 (bacteria) / Gene: tnmJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A125SA13 #2: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl pH 8.5, and 25% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→29.02 Å / Num. obs: 98178 / % possible obs: 93.52 % / Redundancy: 1.54 % / CC1/2: 0.986 / Rmerge(I) obs: 0.05692 / Net I/σ(I): 9.96 |
Reflection shell | Resolution: 1.5→1.556 Å / Rmerge(I) obs: 0.08965 / Num. unique obs: 7779 / CC1/2: 0.927 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F8C Resolution: 1.5→29.02 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→29.02 Å
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Refine LS restraints |
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LS refinement shell |
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