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Yorodumi- PDB-5msz: Lytic Polysaccharide Monooxygenase AA15 from Thermobia domestica ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5msz | ||||||
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Title | Lytic Polysaccharide Monooxygenase AA15 from Thermobia domestica in the Cu(I) State | ||||||
Components | Thermobia domestica domestica AA15 | ||||||
Keywords | OXIDOREDUCTASE / Lytic Polysaccharide Monooxygenase / CAZy / AA15 / Cellulose / Chitin / Copper | ||||||
Function / homology | Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / COPPER (I) ION / Thermobia domestica domestica AA15 Function and homology information | ||||||
Biological species | Thermobia domestica (firebrat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å | ||||||
Authors | Hemsworth, G.R. / Sabbadin, F. / Ciano, L. / Henrissat, B. / Dupree, P. / Tryfona, T. / Besser, K. / Elias, L. / Pesante, G. / Li, Y. ...Hemsworth, G.R. / Sabbadin, F. / Ciano, L. / Henrissat, B. / Dupree, P. / Tryfona, T. / Besser, K. / Elias, L. / Pesante, G. / Li, Y. / Dowle, A. / Bates, R. / Gomez, L. / Hallam, R. / Davies, G.J. / Walton, P.H. / Bruce, N.C. / McQueen-Mason, S. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion. Authors: Sabbadin, F. / Hemsworth, G.R. / Ciano, L. / Henrissat, B. / Dupree, P. / Tryfona, T. / Marques, R.D.S. / Sweeney, S.T. / Besser, K. / Elias, L. / Pesante, G. / Li, Y. / Dowle, A.A. / Bates, ...Authors: Sabbadin, F. / Hemsworth, G.R. / Ciano, L. / Henrissat, B. / Dupree, P. / Tryfona, T. / Marques, R.D.S. / Sweeney, S.T. / Besser, K. / Elias, L. / Pesante, G. / Li, Y. / Dowle, A.A. / Bates, R. / Gomez, L.D. / Simister, R. / Davies, G.J. / Walton, P.H. / Bruce, N.C. / McQueen-Mason, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5msz.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5msz.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 5msz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5msz_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 5msz_full_validation.pdf.gz | 437.6 KB | Display | |
Data in XML | 5msz_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 5msz_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/5msz ftp://data.pdbj.org/pub/pdb/validation_reports/ms/5msz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22426.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobia domestica (firebrat) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R2JFH0*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-CU1 / | #4: 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: 1.99 Å3/Da / Density % sol: 38.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium citrate pH 5.5, 0.1 M LiCl, and 10 to 25% w/v polyethylene glycol 6000 (PEG-6000) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 4, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Entry-ID: 5MSZ
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Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.1→56.87 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.949 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / 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: 15.725 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→56.87 Å
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Refine LS restraints |
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