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- PDB-2jf6: Structure of inactive mutant of Strictosidine Glucosidase in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jf6 | ||||||
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Title | Structure of inactive mutant of Strictosidine Glucosidase in complex with strictosidine | ||||||
![]() | STRICTOSIDINE-O-BETA-D-GLUCOSIDASE | ||||||
![]() | HYDROLASE / ALKALOID | ||||||
Function / homology | ![]() 3alpha(S)-strictosidine beta-glucosidase / strictosidine beta-glucosidase activity / alkaloid biosynthetic process / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barleben, L. / Panjikar, S. / Ruppert, M. / Koepke, J. / Stockigt, J. | ||||||
![]() | ![]() Title: Molecular Architecture of Strictosidine Glucosidase - the Gateway to the Biosynthesis of the Monoterpenoid Indole Alkaloid Family Authors: Barleben, L. / Panjikar, S. / Ruppert, M. / Koepke, J. / Stockigt, J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.2 KB | Display | ![]() |
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PDB format | ![]() | 159 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 53.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jf7SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.791608, 0.611021, 0.00323), Vector: |
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Components
#1: Protein | Mass: 60959.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8GU20, 3alpha(S)-strictosidine beta-glucosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 4.27 % / Description: NONE |
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Crystal grow | Details: 0.35 M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH 4.6 11% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8048 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→20 Å / Num. obs: 32951 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 28.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.82→2.97 Å / Redundancy: 28 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.6 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JF7 Resolution: 2.82→20 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.813 / SU B: 23.7 / SU ML: 0.347 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.82→20 Å
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Refine LS restraints |
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