+Open data
-Basic information
Entry | Database: PDB / ID: 6q8n | |||||||||
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Title | GH10 endo-xylanase in complex with xylobiose epoxide inhibitor | |||||||||
Components | Beta-xylanaseXylanase | |||||||||
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: 1.76 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 | 6q8n.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q8n.ent.gz | 120.5 KB | Display | PDB format |
PDBx/mmJSON format | 6q8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q8n ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q8n | HTTPS FTP |
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-Related structure data
Related structure data | 6q7iC 6q7jC 6q8mC 6qe8C 3u7bS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#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 |
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-Sugars , 2 types, 6 molecules
#2: Sugar | ChemComp-NAG / #6: Sugar | |
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-Non-polymers , 4 types, 661 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #7: 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). Co-crystallisation with xylobiose epoxide inhibitor. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→62.57 Å / Num. obs: 81568 / % possible obs: 99.96 % / Redundancy: 7.95 % / Rpim(I) all: 0.044 / Net I/σ(I): 10.69 |
Reflection shell | Resolution: 1.76→1.79 Å / Mean I/σ(I) obs: 1.07 / Num. unique obs: 4016 / Rpim(I) all: 0.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U7B Resolution: 1.76→62.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.601 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / 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: 24.914 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→62.57 Å
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