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- PDB-6rs4: Structure of tabersonine synthase - an alpha-beta hydrolase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rs4 | |||||||||
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Title | Structure of tabersonine synthase - an alpha-beta hydrolase from Catharanthus roseus | |||||||||
![]() | Tabersonine synthase | |||||||||
![]() | HYDROLASE / alkaloid / TABERSONINE / natural product / biosynthesis / alpha/beta hydrolase fold | |||||||||
Function / homology | ![]() Lyases / alkaloid metabolic process / hydrolase activity / lyase activity / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Caputi, L. / Franke, J. / Bussey, K. / Farrow, S.C. / Curcino Vieira, I.J. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis of cycloaddition in biosynthesis of iboga and aspidosperma alkaloids. Authors: Caputi, L. / Franke, J. / Bussey, K. / Farrow, S.C. / Vieira, I.J.C. / Stevenson, C.E.M. / Lawson, D.M. / O'Connor, S.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 299.1 KB | Display | ![]() |
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PDB format | ![]() | 242.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.6 KB | Display | ![]() |
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Full document | ![]() | 457.9 KB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 49.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rj8C ![]() 6rt8C ![]() 2o7rS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36256.051 Da / Num. of mol.: 2 Mutation: Native N-terminal MET is replaced by a GLY-PRO dipeptide left over from cleavage of the affinity tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: TS, HL2 / Plasmid: pOPINF / Production host: ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: NULL / PH range: NULL / Temp details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→59.95 Å / Num. obs: 177427 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 10.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.046 / Rrim(I) all: 0.12 / Net I/σ(I): 10.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2O7R Resolution: 1.3→59.95 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.907 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.48 Å2 / Biso mean: 16.166 Å2 / Biso min: 6.81 Å2
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Refinement step | Cycle: final / Resolution: 1.3→59.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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