+Open data
-Basic information
Entry | Database: PDB / ID: 6ydg | ||||||
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Title | X-ray structure of LPMO | ||||||
Components | Auxiliary activity 9 | ||||||
Keywords | METAL BINDING PROTEIN / Lytic Polysaccharide Monooxygenase / Complex / cellotetraose | ||||||
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: 1.9 Å | ||||||
Authors | Tandrup, T. / Tryfona, T. / Frandsen, K.E.H. / Johansen, K.S. / Dupree, P. / Lo Leggio, L. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Biochemistry / Year: 2020 Title: Oligosaccharide Binding and Thermostability of Two Related AA9 Lytic Polysaccharide Monooxygenases. Authors: Tandrup, T. / Tryfona, T. / Frandsen, K.E.H. / Johansen, K.S. / Dupree, P. / Lo Leggio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ydg.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydg.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ydg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydg ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydg | HTTPS FTP |
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-Related structure data
Related structure data | 6ydcC 6yddC 6ydeC 6ydfC 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) / References: UniProt: A0A0S2GKZ1 |
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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, 196 molecules
#3: Chemical | ChemComp-CU / |
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#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 3.27 Å3/Da / Density % sol: 62.41 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 3.3 M NaCl, 0.1 M citric acid pH 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 27327 / % possible obs: 100 % / Redundancy: 17.14 % / CC1/2: 1 / Net I/σ(I): 26.32 |
Reflection shell | Resolution: 1.9→1.95 Å / Num. unique obs: 1986 / CC1/2: 0.547 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ACH Resolution: 1.9→50 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 78.45 Å2 / Biso mean: 28.1531 Å2 / Biso min: 13.95 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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