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Yorodumi- PDB-6zea: Strictosidine Synthase from Catharanthus roseus in complex with r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zea | ||||||
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Title | Strictosidine Synthase from Catharanthus roseus in complex with racemic 1-methyl-2,3,4,9-tetrahydro-1H-beta-carboline | ||||||
Components | Strictosidine synthase | ||||||
Keywords | LYASE / C-C bond / alkaloid | ||||||
Function / homology | Function and homology information strictosidine synthase / strictosidine synthase activity / alkaloid metabolic process / vacuole / biosynthetic process Similarity search - Function | ||||||
Biological species | Catharanthus roseus (Madagascar periwinkle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Eger, E. / Sharma, M. / Kroutil, W. / Grogan, G. | ||||||
Citation | Journal: To Be Published Title: Strictosidine Synthase from Catharanthus roseus in complex with racemic 1-methyl-2,3,4,9-tetrahydro-1H-beta-carboline Authors: Eger, E. / Sharma, M. / Kroutil, W. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zea.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zea.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zea_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6zea_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6zea_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 6zea_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/6zea ftp://data.pdbj.org/pub/pdb/validation_reports/ze/6zea | HTTPS FTP |
-Related structure data
Related structure data | 6s5mS 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: 35760.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle) Gene: STR1, SSS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18417, strictosidine synthase | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-QGH / ( | #4: Chemical | ChemComp-QGK / ( | #5: 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: 2.43 Å3/Da / Density % sol: 49.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium chloride, HEPES pH 7.0, 20% PEG 6000 (w/v) |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→43.47 Å / Num. obs: 51780 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.54→1.58 Å / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3756 / CC1/2: 0.58 / Rpim(I) all: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S5M Resolution: 1.54→43.47 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.069 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 116.62 Å2 / Biso mean: 34.283 Å2 / Biso min: 15.95 Å2
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Refinement step | Cycle: final / Resolution: 1.54→43.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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