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Yorodumi- PDB-6s5m: Strictosidine Synthase from Ophiorrhiza pumila in complex with (S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s5m | ||||||
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Title | Strictosidine Synthase from Ophiorrhiza pumila in complex with (S)-1-n-propyl-2,3,4,9-tetrahydro-1H-beta-carboline | ||||||
Components | Strictosidine synthase | ||||||
Keywords | LYASE / alkaloid / C-C bond / Pictet-Spenglerase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ophiorrhiza pumila (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Eger, E. / Sharma, M. / Kroutil, W. / Grogan, G. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Inverted Binding of Non-natural Substrates in Strictosidine Synthase Leads to a Switch of Stereochemical Outcome in Enzyme-Catalyzed Pictet-Spengler Reactions. Authors: Eger, E. / Simon, A. / Sharma, M. / Yang, S. / Breukelaar, W.B. / Grogan, G. / Houk, K.N. / Kroutil, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s5m.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s5m.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 6s5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/6s5m ftp://data.pdbj.org/pub/pdb/validation_reports/s5/6s5m | HTTPS FTP |
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-Related structure data
Related structure data | 6s5jC 6s5qC 6s5uC 2fp9S 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: 36769.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ophiorrhiza pumila (plant) / Gene: str / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle / References: UniProt: Q94LW9 |
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#2: Chemical | ChemComp-KWH / ( |
#3: 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: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCL pH 8.0, 0.3 M NH4Cl, 20% PEG 6K |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→54.84 Å / Num. obs: 28720 / % possible obs: 98.9 % / Redundancy: 4.1 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.04 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1858 / CC1/2: 0.95 / Rpim(I) all: 0.44 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FP9 Resolution: 1.9→54.84 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.417 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.142 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: 100.67 Å2 / Biso mean: 48.876 Å2 / Biso min: 33.24 Å2
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Refinement step | Cycle: final / Resolution: 1.9→54.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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