+Open data
-Basic information
Entry | Database: PDB / ID: 6ydc | ||||||
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Title | X-ray structure of LPMO | ||||||
Components | LPMO lytic polysaccharide monooxygenase | ||||||
Keywords | METAL BINDING PROTEIN / Lytic Polysaccharide Monooxygenase / Complex / cellotetraose | ||||||
Function / homology | Function and homology information cellulase / monooxygenase activity / hydrolase activity / extracellular region Similarity search - Function | ||||||
Biological species | Collariella virescens (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 6ydc.cif.gz | 226.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydc.ent.gz | 179.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ydc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydc ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydc | HTTPS FTP |
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-Related structure data
Related structure data | 6yddC 6ydeC 6ydfC 6ydgC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 27791.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Collariella virescens (fungus) / Gene: aa9 / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A223GEC9 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | #3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotriose | |
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-Non-polymers , 3 types, 1464 molecules
#4: Chemical | ChemComp-CU / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-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: 2.95 Å3/Da / Density % sol: 58.25 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M NaCl, 0.1 M HEPES pH 6.5, 1.5 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.96 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 85419 / % possible obs: 98.4 % / Redundancy: 4.55 % / CC1/2: 0.989 / Net I/σ(I): 5.54 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.16 % / Mean I/σ(I) obs: 1.44 / Num. unique obs: 6184 / CC1/2: 0.544 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ACH Resolution: 2→50 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 61.24 Å2 / Biso mean: 14.8197 Å2 / Biso min: 2.27 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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