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Yorodumi- PDB-6z82: Thalictrum flavumn Norcoclaurine synthase point mutant in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z82 | ||||||||||||
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Title | Thalictrum flavumn Norcoclaurine synthase point mutant in complex with a transition state analoge | ||||||||||||
Components | S-norcoclaurine synthase | ||||||||||||
Keywords | LYASE / PICTET SPENGLER CONDENSATION / DOPAMINE | ||||||||||||
Function / homology | (S)-norcoclaurine synthase / (S)-norcoclaurine synthase activity / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / alkaloid metabolic process / START-like domain superfamily / defense response / 4-[2-[(phenylmethyl)amino]ethyl]benzene-1,2-diol / S-norcoclaurine synthase Function and homology information | ||||||||||||
Biological species | Thalictrum flavum subsp. glaucum (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Roddan, R. / Sula, A. / Keep, N.H. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Commun Chem / Year: 2020 Title: Single step syntheses of (1S)-aryl-tetrahydroisoquinolines by norcoclaurine synthases Authors: Roddan, R. / Sula, A. / Mendez-Sanchez, D. / Subrizi, F. / Lichman, B.R. / Broomfield, J. / Richter, M. / Andexer, J.N. / Ward, J.M. / Keep, N.H. / Hailes, H.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z82.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z82.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 6z82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/6z82 ftp://data.pdbj.org/pub/pdb/validation_reports/z8/6z82 | HTTPS FTP |
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-Related structure data
Related structure data | 5nonS 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
#1: Protein | Mass: 18206.000 Da / Num. of mol.: 1 / Mutation: M97V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thalictrum flavum subsp. glaucum (plant) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q67A25, (S)-norcoclaurine synthase |
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#2: Chemical | ChemComp-QBW / |
#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: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% w/v PEG 1500, 20% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→54.27 Å / Num. obs: 7696 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 69.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.012 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 719 / CC1/2: 0.975 / Rpim(I) all: 0.171 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NON Resolution: 2.3→54.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 21.901 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.349 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.78 Å2 / Biso mean: 79.715 Å2 / Biso min: 48.02 Å2
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Refinement step | Cycle: final / Resolution: 2.3→54.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.356 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -1.7935 Å / Origin y: 20.5881 Å / Origin z: 7.1906 Å
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