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Yorodumi- PDB-6sxr: E221Q mutant of GH54 a-l-arabinofuranosidase soaked with 4-nitrop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sxr | |||||||||
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Title | E221Q mutant of GH54 a-l-arabinofuranosidase soaked with 4-nitrophenyl a-l-arabinofuranoside | |||||||||
Components | Alpha-L-arabinofuranosidase B | |||||||||
Keywords | HYDROLASE / Michaelis 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 IFO 4308 (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 | 6sxr.cif.gz | 193.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sxr.ent.gz | 155.5 KB | Display | PDB format |
PDBx/mmJSON format | 6sxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sxr_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6sxr_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6sxr_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 6sxr_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/6sxr ftp://data.pdbj.org/pub/pdb/validation_reports/sx/6sxr | HTTPS FTP |
-Related structure data
Related structure data | 6sxsC 6sxtC 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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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: 50882.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus kawachii IFO 4308 (mold) / Gene: abfB, AKAW_08685 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) References: UniProt: Q8NK89, non-reducing end alpha-L-arabinofuranosidase |
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-Sugars , 3 types, 5 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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#3: Sugar | ChemComp-NAG / |
#6: Sugar |
-Non-polymers , 7 types, 381 molecules
#4: Chemical | #5: Chemical | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-PEG / #9: Chemical | ChemComp-PGE / | #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 % 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, 0.4 M Li2SO4 |
-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 19, 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: 1.64→93.28 Å / Num. obs: 99211 / % possible obs: 98.2 % / Redundancy: 12.6 % / CC1/2: 1 / Rrim(I) all: 0.129 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4864 / CC1/2: 0.5 / Rrim(I) all: 2.319 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WD3 Resolution: 1.64→93.28 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.064 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: 26.156 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→93.28 Å
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Refine LS restraints |
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LS refinement shell |
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