+
Open data
-
Basic information
Entry | Database: PDB / ID: 3zj6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal of Raucaffricine Glucosidase in complex with inhibitor | ||||||
![]() | RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE | ||||||
![]() | HYDROLASE / RG / INHIBITOR / 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. / Lin, H. / Panjikar, S. / Ruppert, M. / Castiglia, A. / Rajendran, C. / Wang, M. / Schuebel, H. / Warzecha, H. / Jaeger, V. / Stoeckigt, J. | ||||||
![]() | ![]() Title: Ligand Structures of Synthetic Deoxa-Pyranosylamines with Raucaffricine and Strictosidine Glucosidases Provide Structural Insights Into Their Binding and Inhibitory Behaviours. Authors: Xia, L. / Lin, H. / Staniek, A. / Panjikar, S. / Ruppert, M. / Hilgers, P. / Williardt, J. / Rajendran, C. / Wang, M. / Warzecha, H. / Jager, V. / Stockigt, J. #1: ![]() 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 |
| ||||||
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. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 383 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 313.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3zj7C ![]() 3zj8C ![]() 4atdS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
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: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 13 - 510 / Label seq-ID: 13 - 510
NCS oper: (Code: given Matrix: (-1, -0.001103, -0.000763), Vector: |
-
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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.5 % / Description: NONE |
---|---|
Crystal grow | Details: 10% PEG4000, 0.3 M AMSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 2006 / Details: MONOCHROMATOR |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8015 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 56755 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Biso Wilson estimate: 38.838 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 4.86 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4ATD Resolution: 2.4→19.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.772 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.183 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.136 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|