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- PDB-5non: Structure of truncated Norcoclaurine Synthase from Thalictrum fla... -
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Basic information
Entry | Database: PDB / ID: 5non | ||||||
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Title | Structure of truncated Norcoclaurine Synthase from Thalictrum flavum with product mimic | ||||||
![]() | S-norcoclaurine synthase | ||||||
![]() | LYASE / Pictet Spengler condensation / Dopamine | ||||||
Function / homology | ![]() (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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sula, A. / Lichman, B.R. / Pesnot, T. / Ward, J.M. / Hailes, H.C. / Keep, N.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221 KB | Display | ![]() |
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PDB format | ![]() | 180.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 18238.064 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PD451 - SR / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.43 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 10% W/V POLYETHYLENE GLYCOL 1000, 10% REMARK 280 W/V POLYETHYLENE GLYCOL 8000 20 MM TRIS, 50 MM NACL, PH 7.5, PH REMARK 280 8.5, 10 mM Ligand |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 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: 1.85→85.85 Å / Num. obs: 50659 / % possible obs: 100 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.032 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.009 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3072 / Rpim(I) all: 0.35 / % possible all: 100 |
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Processing
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Refinement | Resolution: 1.85→86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.774 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.125 / 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: 36.86 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→86 Å
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Refine LS restraints |
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