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Yorodumi- PDB-7e36: A [6+4]-cycloaddition adduct is the biosynthetic intermediate in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7.0E+36 | |||||||||||||||||||||||||||
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Title | A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis | |||||||||||||||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / nargenicin / BIOSYNTHETIC PROTEIN / Oxidase | |||||||||||||||||||||||||||
Function / homology | Nitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / FMN-dependent oxidoreductase (Nitrilotriacetate monooxygenase family) / Alkanesulfonate monooxygenase SsuD/methylene tetrahydromethanopterin reductase-like flavin-dependent oxidoreductase (Luciferase family) Function and homology information | |||||||||||||||||||||||||||
Biological species | Nocardia tenerifensis (bacteria) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||||||||||||||||||||
Authors | Zhang, B. / Ge, H.M. | |||||||||||||||||||||||||||
Funding support | China, 8items
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Citation | Journal: Nat Commun / Year: 2021 Title: A [6+4]-cycloaddition adduct is the biosynthetic intermediate in streptoseomycin biosynthesis. Authors: Wang, K.B. / Wang, W. / Zhang, B. / Wang, X. / Chen, Y. / Zhu, H.J. / Liang, Y. / Tan, R.X. / Ge, H.M. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e36.cif.gz | 307.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e36.ent.gz | 244.8 KB | Display | PDB format |
PDBx/mmJSON format | 7e36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e36_validation.pdf.gz | 481.7 KB | Display | wwPDB validaton report |
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Full document | 7e36_full_validation.pdf.gz | 489.4 KB | Display | |
Data in XML | 7e36_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 7e36_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/7e36 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/7e36 | HTTPS FTP |
-Related structure data
Related structure data | 1tvlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 34339.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nocardia tenerifensis (bacteria) / Strain: NBRC 101015 / Gene: DFR70_1157 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A318JWT9 |
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#2: Protein | Mass: 46418.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nocardia tenerifensis (bacteria) / Strain: NBRC 101015 / Gene: DFR70_1156 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A318JQQ2 |
-Non-polymers , 6 types, 504 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-MES / | #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.6 M magnesium sulfate, 0.1 M MES monohydrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→75.54 Å / Num. obs: 54007 / % possible obs: 99.7 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Net I/σ(I): 7.3 / Num. measured all: 180663 / Scaling rejects: 305 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TVL Resolution: 2→51 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.99 / Stereochemistry target values: ML
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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 max: 152.67 Å2 / Biso mean: 33.5148 Å2 / Biso min: 13.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→51 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 19.8445 Å / Origin y: 1.5814 Å / Origin z: 12.2308 Å
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Refinement TLS group | Selection details: all |