+Open data
-Basic information
Entry | Database: PDB / ID: 6q8m | ||||||
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Title | GH10 endo-xylanase | ||||||
Components | Beta-xylanase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus aculeatus ATCC 16872 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Davies, G.J. / Rowland, R.J. / Wu, L. / Moroz, O. / Blagova, E. | ||||||
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 | 6q8m.cif.gz | 165.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q8m.ent.gz | 127.6 KB | Display | PDB format |
PDBx/mmJSON format | 6q8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q8m ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q8m | HTTPS FTP |
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-Related structure data
Related structure data | 6q7iC 6q7jC 6q8nC 6qe8C 3u7bS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42905.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus aculeatus ATCC 16872 (mold) Gene: ASPACDRAFT_127619 / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A1L9WG58, endo-1,4-beta-xylanase #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-K / #5: 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: 2.19 Å3/Da / Density % sol: 43.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium/potassium phosphate (pH 6.9) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97965 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97965 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→70.09 Å / Num. obs: 142509 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.032 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.42→1.44 Å / Mean I/σ(I) obs: 2.3 / Rpim(I) all: 1.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U7B Resolution: 1.42→70.09 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.985 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.052 / 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: 13.3 Å2
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Refinement step | Cycle: 1 / Resolution: 1.42→70.09 Å
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Refine LS restraints |
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