[English] 日本語
Yorodumi- PDB-5non: Structure of truncated Norcoclaurine Synthase from Thalictrum fla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5non | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of truncated Norcoclaurine Synthase from Thalictrum flavum with product mimic | ||||||
Components | S-norcoclaurine synthase | ||||||
Keywords | LYASE / Pictet Spengler condensation / Dopamine | ||||||
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 subsp. glaucum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å | ||||||
Authors | Sula, A. / Lichman, B.R. / Pesnot, T. / Ward, J.M. / Hailes, H.C. / Keep, N.H. | ||||||
Citation | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5non.cif.gz | 221 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5non.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 5non.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5non_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5non_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5non_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 5non_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/5non ftp://data.pdbj.org/pub/pdb/validation_reports/no/5non | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
|
-Components
#1: Protein | Mass: 18238.064 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thalictrum flavum subsp. glaucum (plant) Plasmid: PD451 - SR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q67A25, (S)-norcoclaurine synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.43 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.85→86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|