+Open data
-Basic information
Entry | Database: PDB / ID: 7v6h | |||||||||
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Title | Crystal Structure of the SpnL | |||||||||
Components | Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase | |||||||||
Keywords | TRANSFERASE / SpnL / Rauhut-Currier reaction / spinosyn A / Saccharopolyspora spinosa / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | Methyltransferase type 11 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Cyclopropane fatty-acyl-phospholipid synthase-like methyltransferase Function and homology information | |||||||||
Biological species | Saccharopolyspora spinosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.054 Å | |||||||||
Authors | Wu, H.-H. / Ko, T.-P. / Liu, H.-W. / Tsai, M.-D. | |||||||||
Funding support | Taiwan, United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Evidence for an Enzyme-Catalyzed Rauhut-Currier Reaction during the Biosynthesis of Spinosyn A. Authors: Choi, S.H. / Jeon, B. / Kim, N. / Wu, H.H. / Ko, T.P. / Ruszczycky, M.W. / Isiorho, E.A. / Liu, Y.N. / Keatinge-Clay, A.T. / Tsai, M.D. / Liu, H.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v6h.cif.gz | 218.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v6h.ent.gz | 183.2 KB | Display | PDB format |
PDBx/mmJSON format | 7v6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/7v6h ftp://data.pdbj.org/pub/pdb/validation_reports/v6/7v6h | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30749.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: A8926_6440 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N3Y640 #2: Chemical | Has ligand of interest | 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: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.3 M sodium citrate, 100 mM Tris-HCl, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 13408 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3.05→3.1 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 8.9 / Num. unique obs: 644 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.054→46.347 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.83 / 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 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.054→46.347 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -38.1683 Å / Origin y: 22.934 Å / Origin z: -5.1144 Å
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Refinement TLS group | Selection details: all |