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Yorodumi- PDB-2vq5: X-ray structure of Norcoclaurine synthase from Thalictrum flavum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vq5 | ||||||
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Title | X-ray structure of Norcoclaurine synthase from Thalictrum flavum in complex with dopamine and hydroxybenzaldehyde | ||||||
Components | S-NORCOCLAURINE SYNTHASE | ||||||
Keywords | LYASE / NORCOCLAURINE SYNTHASE / S- NORCOCLAURINE BIOSYNTHESIS / DOPAMINE / HYDROXYBENZALDEHYDE | ||||||
Function / homology | Function and homology information (S)-norcoclaurine synthase / (S)-norcoclaurine synthase activity / alkaloid metabolic process / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | THALICTRUM FLAVUM (yellow meadow-rue) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Ilari, A. / Franceschini, S. / Bonamore, A. / Boffi, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural Basis of Enzymatic S-Norcoclaurine Biosynthesis. Authors: Ilari, A. / Franceschini, S. / Bonamore, A. / Arenghi, F. / Botta, B. / Macone, A. / Pasquo, A. / Bellucci, L. / Boffi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vq5.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vq5.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vq5_validation.pdf.gz | 475.6 KB | Display | wwPDB validaton report |
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Full document | 2vq5_full_validation.pdf.gz | 482.9 KB | Display | |
Data in XML | 2vq5_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 2vq5_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vq5 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vq5 | HTTPS FTP |
-Related structure data
Related structure data | 2vneSC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 22606.209 Da / Num. of mol.: 2 / Fragment: RESIDUES 16-210 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE PROTEIN LACKS THE FIRST 15 RESIDUES AND IS HIS-TAGGED AT THE C-TERMINUS. Source: (gene. exp.) THALICTRUM FLAVUM (yellow meadow-rue) / Plasmid: PET22-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q67A25, (S)-norcoclaurine synthase |
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-Non-polymers , 5 types, 183 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-LDP / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, THR 16 TO MSE ENGINEERED RESIDUE IN CHAIN A, ILE 17 TO THR ...ENGINEERED |
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Sequence details | DATABASE NAME NCBI THE PROTEIN HAS SIX HIS AT THE C- TERMINUS AND LACKS THE FIRST 15 RESIDUES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: AMMONIUM SULFATE 1.4-1.8 M, NACL 0.2 M, ACETATE BUFFER PH 4.0-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 30118 / % possible obs: 97.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 98.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VNE Resolution: 2.09→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.069 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 37.381 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→50 Å
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