+Open data
-Basic information
Entry | Database: PDB / ID: 5nlr | |||||||||
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Title | Auxiliary activity 9 | |||||||||
Components | Auxiliary activity 9 | |||||||||
Keywords | OXIDOREDUCTASE / Enzyme | |||||||||
Function / homology | Function and homology information cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Lentinus similis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Frandsen, K.E.H. / Poulsen, J.-C.N. / Tandrup, T. / Lo Leggio, L. | |||||||||
Funding support | Denmark, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Structural and electronic determinants of lytic polysaccharide monooxygenase reactivity on polysaccharide substrates. Authors: Simmons, T.J. / Frandsen, K.E.H. / Ciano, L. / Tryfona, T. / Lenfant, N. / Poulsen, J.C. / Wilson, L.F.L. / Tandrup, T. / Tovborg, M. / Schnorr, K. / Johansen, K.S. / Henrissat, B. / Walton, ...Authors: Simmons, T.J. / Frandsen, K.E.H. / Ciano, L. / Tryfona, T. / Lenfant, N. / Poulsen, J.C. / Wilson, L.F.L. / Tandrup, T. / Tovborg, M. / Schnorr, K. / Johansen, K.S. / Henrissat, B. / Walton, P.H. / Lo Leggio, L. / Dupree, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nlr.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nlr.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/5nlr ftp://data.pdbj.org/pub/pdb/validation_reports/nl/5nlr | HTTPS FTP |
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-Related structure data
Related structure data | 5nkwC 5nlnC 5nloC 5nlpC 5nlqC 5nlsC 5nltC 5achS 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: 25272.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lentinus similis (fungus) / Production host: Aspergillus oryzae (mold) / Variant (production host): MT3568 / References: UniProt: A0A0S2GKZ1, Oxidoreductases |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 281 molecules
#3: Chemical | ChemComp-CU / | ||
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#5: Chemical | ChemComp-CL / #6: 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: 3.21 Å3/Da / Density % sol: 61.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 3.5 M NaCl 0.1 M citric acid, pH3.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03841 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 17, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03841 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 23096 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / CC1/2: 0.996 / Rrim(I) all: 0.238 / Net I/σ(I): 12.31 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 11.39 % / Mean I/σ(I) obs: 1.85 / Num. unique obs: 1680 / CC1/2: 0.498 / Rrim(I) all: 1.64 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ACH Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.867 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.137 / 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: 24.172 Å2
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Refinement step | Cycle: 1 / Resolution: 2→50 Å
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Refine LS restraints |
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