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Yorodumi- PDB-5l77: A glycoside hydrolase mutant with an unreacted activity based pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l77 | |||||||||
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Title | A glycoside hydrolase mutant with an unreacted activity based probe bound | |||||||||
Components | beta-glucuronidase | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Acidobacterium capsulatum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | |||||||||
Authors | Jin, Y. / Wu, L. / Jiang, J.B. / Overkleeft, H.S. / Davies, G.J. | |||||||||
Funding support | United Kingdom, 1items
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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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l77.cif.gz | 212.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l77.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 5l77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/5l77 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/5l77 | HTTPS FTP |
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-Related structure data
Related structure data | 5g0qC 5l9yC 5l9zC 5la4C 5la7C 3vyoS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52984.926 Da / Num. of mol.: 1 / Mutation: E287Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidobacterium capsulatum (bacteria) / Gene: ACP_2665 / Plasmid: PET-28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: C1F2K5 |
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-Non-polymers , 5 types, 491 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GUX / ( | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-GOL / | #6: 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: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 12 mg/mL protein stock in mixed 1:1 with 1.2 M NaH2PO4/K2HPO4 (1:9 v/v) at 293 K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→28.88 Å / Num. obs: 126454 / % possible obs: 89.8 % / Redundancy: 3.9 % / CC1/2: 0.998 / Net I/σ(I): 13.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VYO Resolution: 1.24→28.88 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.48 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.698 Å2
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Refinement step | Cycle: 1 / Resolution: 1.24→28.88 Å
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Refine LS restraints |
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