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- PDB-4a3y: Crystal structure of Raucaffricine glucosidase from ajmaline bios... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a3y | ||||||
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Title | Crystal structure of Raucaffricine glucosidase from ajmaline biosynthesis pathway | ||||||
![]() | RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE | ||||||
![]() | HYDROLASE / ALKALOID | ||||||
Function / homology | ![]() vomilenine glucosyltransferase / raucaffricine beta-glucosidase / raucaffricine beta-glucosidase activity / vomilenine glucosyltransferase activity / alkaloid biosynthetic process / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xia, L. / Ruppert, M. / Wang, M. / Panjikar, S. / Barleben, L. / Rajendran, C. / Lin, H. / Stoeckigt, J. | ||||||
![]() | ![]() Title: Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity. Authors: Xia, L. / Ruppert, M. / Wang, M. / Panjikar, S. / Lin, H. / Rajendran, C. / Barleben, L. / 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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 | ![]() | 382.6 KB | Display | ![]() |
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PDB format | ![]() | 313.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3u57C ![]() 3u5uC ![]() 3u5yC ![]() 2jf7S 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 2 / Auth seq-ID: 13 - 512 / Label seq-ID: 13 - 512
NCS oper: (Code: given Matrix: (-1, -0.001019, -0.000687), Vector: |
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Components
#1: Protein | Mass: 61004.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.01 TO 0.3 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5 TO 5.0, 9 TO 12% (W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: May 18, 2006 / Details: MIRROR |
Radiation | Monochromator: SI 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 76299 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.15→2.3 Å / Redundancy: 15 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.4 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JF7 Resolution: 2.15→19.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.499 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.144 / 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: 36.186 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→19.99 Å
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Refine LS restraints |
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