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Yorodumi- PDB-6rp3: Truncated Norcoclaurine synthase with reaction intermediate mimic -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rp3 | ||||||
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Title | Truncated Norcoclaurine synthase with reaction intermediate mimic | ||||||
Components | S-norcoclaurine synthase | ||||||
Keywords | LYASE / tetrahydroisoquinoline synthase / biotransformation | ||||||
Function / homology | Function and homology information (S)-norcoclaurine synthase / (S)-norcoclaurine synthase activity / alkaloid metabolic process / defense response Similarity search - Function | ||||||
Biological species | Thalictrum flavum subsp. glaucum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Keep, N.H. / Roddan, R. / Sula, A. | ||||||
Citation | Journal: Acs Catalysis / Year: 2019 Title: Acceptance and Kinetic Resolution of alpha-Methyl-Substituted Aldehydes by Norcoclaurine Synthases Authors: Roddan, R. / Gygli, G. / Sula, A. / Lichman, B.R. / Pleiss, J. / Ward, J.M. / Keep, N.H. / Hailes, H.C. #1: Journal: Biochemistry / Year: 2017 Title: Structural Evidence for the Dopamine-First Mechanism of Norcoclaurine Synthase. Authors: Lichman, B.R. / Sula, A. / Pesnot, T. / Hailes, H.C. / Ward, J.M. / Keep, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rp3.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rp3.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/6rp3 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/6rp3 | HTTPS FTP |
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-Related structure data
Related structure data | 5n8qS 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: 18238.064 Da / Num. of mol.: 1 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-KCZ / | ||||
#3: Chemical | #4: 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: 2.32 Å3/Da / Density % sol: 47.04 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22% polyethylene glycol monomethylether 5000, 80 mM Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→43.5 Å / Num. obs: 15507 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Net I/σ(I): 10.14 |
Reflection shell | Resolution: 1.81→1.86 Å / Redundancy: 5.8 % / Rmerge(I) obs: 2.045 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1116 / CC1/2: 0.642 / Rpim(I) all: 0.864 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N8Q Resolution: 1.81→43.49 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.953 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.136 / 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: 107.18 Å2 / Biso mean: 46.437 Å2 / Biso min: 21.68 Å2
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Refinement step | Cycle: final / Resolution: 1.81→43.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.856 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 1.479 Å / Origin y: -20.377 Å / Origin z: 6.995 Å
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