+Open data
-Basic information
Entry | Database: PDB / ID: 3zj6 | ||||||
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Title | Crystal of Raucaffricine Glucosidase in complex with inhibitor | ||||||
Components | RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE | ||||||
Keywords | HYDROLASE / RG / INHIBITOR / ALKALOID | ||||||
Function / homology | Function and homology information vomilenine glucosyltransferase / raucaffricine beta-glucosidase / raucaffricine beta-glucosidase activity / vomilenine glucosyltransferase activity / alkaloid biosynthetic process / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | RAUVOLFIA SERPENTINA (serpentwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Xia, L. / Lin, H. / Panjikar, S. / Ruppert, M. / Castiglia, A. / Rajendran, C. / Wang, M. / Schuebel, H. / Warzecha, H. / Jaeger, V. / Stoeckigt, J. | ||||||
Citation | Journal: J.Enzyme.Inhib.Med.Chem. / Year: 2015 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: Journal: Acs Chem.Biol. / Year: 2012 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zj6.cif.gz | 383 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zj6.ent.gz | 313.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/3zj6 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/3zj6 | HTTPS FTP |
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-Related structure data
Related structure data | 3zj7C 3zj8C 4atdS C: citing same article (ref.) 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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2 |
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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: 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.) RAUVOLFIA SERPENTINA (serpentwood) / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: Q9SPP9, raucaffricine beta-glucosidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.5 % / Description: NONE |
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Crystal grow | Details: 10% PEG4000, 0.3 M AMSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8015 |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
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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: 43.136 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.86 Å
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Refine LS restraints |
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