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- PDB-5g0q: beta-glucuronidase with an activity-based probe (N-alkyl cyclophe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g0q | ||||||
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Title | beta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol aziridine) bound | ||||||
![]() | BETA-GLUCURONIDASE | ||||||
![]() | HYDROLASE / GH79 / BETA-GLUCURONIDASE / ACTIVITY-BASED PROBE / RETAINING ENZYME | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, Y. / Wu, L. / Jiang, J.B. / Overkleeft, H.S. / Davies, G.J. | ||||||
![]() | ![]() Title: Activity-based probes for functional interrogation of retaining beta-glucuronidases. Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / ...Authors: Wu, L. / Jiang, J. / Jin, Y. / Kallemeijn, W.W. / Kuo, C.L. / Artola, M. / Dai, W. / van Elk, C. / van Eijk, M. / van der Marel, G.A. / Codee, J.D.C. / Florea, B.I. / Aerts, J.M.F.G. / Overkleeft, H.S. / Davies, G.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" 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 | ![]() | 197.8 KB | Display | ![]() |
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PDB format | ![]() | 157.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 709.1 KB | Display | ![]() |
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Full document | ![]() | 710.3 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l77C ![]() 5l9yC ![]() 5l9zC ![]() 5la4C ![]() 5la7C ![]() 3vo0S 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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Unit cell |
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Components
#1: Protein | Mass: 50814.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-IF6 / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.77 % / Description: NONE |
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Crystal grow | pH: 8.6 / Details: 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→42.6 Å / Num. obs: 59263 / % possible obs: 99.5 % / Observed criterion σ(I): 2.2 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3VO0 Resolution: 1.65→74.64 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.765 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.074 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→74.64 Å
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Refine LS restraints |
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