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Yorodumi- PDB-6j1n: Anisodus acutangulus type III polyketide sythase AaPKS2 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j1n | ||||||
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Title | Anisodus acutangulus type III polyketide sythase AaPKS2 in complex with 4-carboxy-3-oxobutanoyl-CoA | ||||||
Components | A. acutangulus PKS2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Anisodus acutangulus / type III polyketide sythase / tropane alkaloids biosynthesis | ||||||
Function / homology | Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Chem-B7X Function and homology information | ||||||
Biological species | Anisodus acutangulus (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.532 Å | ||||||
Authors | Fang, C.L. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Tropane alkaloids biosynthesis involves an unusual type III polyketide synthase and non-enzymatic condensation. Authors: Huang, J.P. / Fang, C. / Ma, X. / Wang, L. / Yang, J. / Luo, J. / Yan, Y. / Zhang, Y. / Huang, S.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j1n.cif.gz | 170 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j1n.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 6j1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j1n_validation.pdf.gz | 916.1 KB | Display | wwPDB validaton report |
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Full document | 6j1n_full_validation.pdf.gz | 926.5 KB | Display | |
Data in XML | 6j1n_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 6j1n_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/6j1n ftp://data.pdbj.org/pub/pdb/validation_reports/j1/6j1n | HTTPS FTP |
-Related structure data
Related structure data | 6j1mC 1cmlS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 46726.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anisodus acutangulus (plant) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta #2: Chemical | #3: Water | ChemComp-HOH / | Has protein modification | 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: 3.47 Å3/Da / Density % sol: 64.57 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 1% tryptone, 0.05M HEPES 7.0, 20% PEG3350, 0.001M Sodium azide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→50 Å / Num. obs: 44048 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 16.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.024 / Rrim(I) all: 0.095 / Rsym value: 0.092 / Χ2: 0.96 / Net I/σ(I): 34.1 |
Reflection shell | Resolution: 2.53→2.57 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.472 / Num. unique obs: 2176 / CC1/2: 0.974 / Rpim(I) all: 0.122 / Rrim(I) all: 0.488 / Rsym value: 0.472 / Χ2: 0.921 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CML Resolution: 2.532→47.149 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 18.02 / 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: 93.75 Å2 / Biso mean: 33.6874 Å2 / Biso min: 15.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.532→47.149 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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