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Yorodumi- PDB-5g0q: beta-glucuronidase with an activity-based probe (N-alkyl cyclophe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g0q | ||||||
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Title | beta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol aziridine) bound | ||||||
Components | BETA-GLUCURONIDASE | ||||||
Keywords | HYDROLASE / GH79 / BETA-GLUCURONIDASE / ACTIVITY-BASED PROBE / RETAINING ENZYME | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ACIDOBACTERIUM CAPSULATUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Jin, Y. / Wu, L. / Jiang, J.B. / Overkleeft, H.S. / Davies, G.J. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g0q.cif.gz | 197.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g0q.ent.gz | 157.4 KB | Display | PDB format |
PDBx/mmJSON format | 5g0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/5g0q ftp://data.pdbj.org/pub/pdb/validation_reports/g0/5g0q | HTTPS FTP |
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-Related structure data
Related structure data | 5l77C 5l9yC 5l9zC 5la4C 5la7C 3vo0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) ACIDOBACTERIUM CAPSULATUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: C1F2K5, beta-glucuronidase | ||
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#2: Chemical | ChemComp-IF6 / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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