+Open data
-Basic information
Entry | Database: PDB / ID: 8.0E+19 | ||||||
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Title | Crystal structure of TnmK1 complexed with TNM H | ||||||
Components | Secreted hydrolase | ||||||
Keywords | HYDROLASE / biosynthesis | ||||||
Function / homology | alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / SUCCINIC ACID / Chem-U8L / Secreted hydrolase Function and homology information | ||||||
Biological species | Streptomyces sp. CB03234 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Liu, Y.-C. / Gui, C. / Shen, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Intramolecular C-C Bond Formation Links Anthraquinone and Enediyne Scaffolds in Tiancimycin Biosynthesis. Authors: Gui, C. / Kalkreuter, E. / Liu, Y.C. / Adhikari, A. / Teijaro, C.N. / 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 | 8e19.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e19.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 8e19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e19_validation.pdf.gz | 844.1 KB | Display | wwPDB validaton report |
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Full document | 8e19_full_validation.pdf.gz | 849 KB | Display | |
Data in XML | 8e19_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 8e19_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/8e19 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/8e19 | HTTPS FTP |
-Related structure data
Related structure data | 8e18SC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 52201.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. CB03234 (bacteria) / Gene: tnmK1, AMK26_32035 / Production host: Streptomyces lividans (bacteria) / References: UniProt: A0A125SA14 |
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#2: Chemical | ChemComp-U8L / ( |
#3: Chemical | ChemComp-EPE / |
#4: Chemical | ChemComp-SIN / |
#5: 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: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES, pH 7.0, 1.0 M succinic acid, pH 7.0, and 1% w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. obs: 31893 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 27.12 Å2 / CC1/2: 0.998 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2.03→2.06 Å / Num. unique obs: 1569 / CC1/2: 0.728 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 8.0E+18 / Resolution: 2.03→29.55 Å / SU ML: 0.2103 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.6859 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: 30.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→29.55 Å
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Refine LS restraints |
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LS refinement shell |
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