+Open data
-Basic information
Entry | Database: PDB / ID: 6sxt | |||||||||
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Title | GH54 a-l-arabinofuranosidase soaked with aziridine inhibitor | |||||||||
Components | Alpha-L-arabinofuranosidase B | |||||||||
Keywords | HYDROLASE / Covalent complex / Arabinofuranosidase / GH54 / Aspergillus | |||||||||
Function / homology | Function and homology information arabinose metabolic process / arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / pectin catabolic process / xylan catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Aspergillus kawachii (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.466 Å | |||||||||
Authors | McGregor, N.G.S. / Davies, G.J. / Nin-Hill, A. / Rovira, C. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-l-Arabinofuranosidases. Authors: McGregor, N.G.S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Haon, M. / Reijngoud, J. / Ram, A. / Rosso, M.N. / van der Marel, G.A. / Codee, J.D.C. / van Wezel, G.P. / Berrin, J.G. / Rovira, ...Authors: McGregor, N.G.S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Haon, M. / Reijngoud, J. / Ram, A. / Rosso, M.N. / van der Marel, G.A. / Codee, J.D.C. / van Wezel, G.P. / Berrin, J.G. / Rovira, C. / 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 | 6sxt.cif.gz | 197.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sxt.ent.gz | 157.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sxt_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6sxt_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6sxt_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 6sxt_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/6sxt ftp://data.pdbj.org/pub/pdb/validation_reports/sx/6sxt | HTTPS FTP |
-Related structure data
Related structure data | 6sxrC 6sxsC 6sxuC 6sxvC 1wd3S 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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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: 50970.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus kawachii (strain NBRC 4308) (mold) Strain: NBRC 4308 / Gene: abfB, AKAW_08685 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 References: UniProt: Q8NK89, non-reducing end alpha-L-arabinofuranosidase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 8 types, 485 molecules
#3: Chemical | ChemComp-ALA / | ||||||||||||
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#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-LXE / [( | #7: Chemical | #8: Chemical | ChemComp-PEG / #9: Chemical | #10: Chemical | ChemComp-EDO / #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density % sol: 34 % Description: Triangular prisms roughly twice as long as the triangle face is tall. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 2:1 protein:well solution. 0.1 M pH 4.5 sodium acetate buffer, 60% PEG400, 0.3 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2019 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.466→85.54 Å / Num. obs: 141273 / % possible obs: 99.3 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.031 / Rrim(I) all: 0.109 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.466→1.491 Å / Redundancy: 10.7 % / Rmerge(I) obs: 2.98 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6968 / CC1/2: 0.367 / Rpim(I) all: 0.94 / Rrim(I) all: 3.13 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WD3 Resolution: 1.466→84.687 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.048 Details: Hydrogens have been added in their 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: 20.664 Å2
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Refinement step | Cycle: LAST / Resolution: 1.466→84.687 Å
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Refine LS restraints |
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LS refinement shell |
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