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Yorodumi- PDB-6qe8: Crystal structure of Aspergillus niger GH11 endoxylanase XynA in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qe8 | ||||||
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Title | Crystal structure of Aspergillus niger GH11 endoxylanase XynA in complex with xylobiose epoxide activity based probe | ||||||
Components | Endo-1,4-beta-xylanase A | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Wu, L. / Rowland, R.J. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2019 Title: Dynamic and Functional Profiling of Xylan-Degrading Enzymes inAspergillusSecretomes Using Activity-Based Probes. Authors: Schroder, S.P. / de Boer, C. / McGregor, N.G.S. / Rowland, R.J. / Moroz, O. / Blagova, E. / Reijngoud, J. / Arentshorst, M. / Osborn, D. / Morant, M.D. / Abbate, E. / Stringer, M.A. / Krogh, ...Authors: Schroder, S.P. / de Boer, C. / McGregor, N.G.S. / Rowland, R.J. / Moroz, O. / Blagova, E. / Reijngoud, J. / Arentshorst, M. / Osborn, D. / Morant, M.D. / Abbate, E. / Stringer, M.A. / Krogh, K.B.R.M. / Raich, L. / Rovira, C. / Berrin, J.G. / van Wezel, G.P. / Ram, A.F.J. / Florea, B.I. / van der Marel, G.A. / Codee, J.D.C. / Wilson, K.S. / Wu, L. / Davies, G.J. / Overkleeft, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qe8.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qe8.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 6qe8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qe8_validation.pdf.gz | 809.9 KB | Display | wwPDB validaton report |
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Full document | 6qe8_full_validation.pdf.gz | 812.1 KB | Display | |
Data in XML | 6qe8_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 6qe8_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/6qe8 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/6qe8 | HTTPS FTP |
-Related structure data
Related structure data | 6q7iC 6q7jC 6q8mC 6q8nC 2qz2S 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
#1: Protein | Mass: 22634.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / References: UniProt: P55329, endo-1,4-beta-xylanase | ||||
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#2: Chemical | ChemComp-MES / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-HZB / ( | #5: 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: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 5.5, 0.1 M NaCl, 1.8 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: I03 / Wavelength: 0.97622 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→47.77 Å / Num. obs: 21974 / % possible obs: 100 % / Redundancy: 23.3 % / Rpim(I) all: 0.033 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 23.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1280 / Rpim(I) all: 0.743 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2qz2 Resolution: 1.79→47.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.084 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.114 / 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: 31.718 Å2
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Refinement step | Cycle: 1 / Resolution: 1.79→47.77 Å
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Refine LS restraints |
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