+Open data
-Basic information
Entry | Database: PDB / ID: 5acj | |||||||||
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Title | X-ray Structure of LPMO | |||||||||
Components | LYTIC POLYSACCHARIDE MONOOXYGENASE | |||||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE | |||||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / cellulase / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | LENTINUS SIMILIS (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Frandsen, K.E.H. / Poulsen, J.N. / Tovborg, M. / Johansen, K.S. / Lo Leggio, L. | |||||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2016 Title: The molecular basis of polysaccharide cleavage by lytic polysaccharide monooxygenases. Authors: Frandsen, K.E. / Simmons, T.J. / Dupree, P. / Poulsen, J.C. / Hemsworth, G.R. / Ciano, L. / Johnston, E.M. / Tovborg, M. / Johansen, K.S. / von Freiesleben, P. / Marmuse, L. / Fort, S. / ...Authors: Frandsen, K.E. / Simmons, T.J. / Dupree, P. / Poulsen, J.C. / Hemsworth, G.R. / Ciano, L. / Johnston, E.M. / Tovborg, M. / Johansen, K.S. / von Freiesleben, P. / Marmuse, L. / Fort, S. / Cottaz, S. / Driguez, H. / Henrissat, B. / Lenfant, N. / Tuna, F. / Baldansuren, A. / Davies, G.J. / Lo Leggio, L. / Walton, P.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5acj.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5acj.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 5acj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5acj_validation.pdf.gz | 738.5 KB | Display | wwPDB validaton report |
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Full document | 5acj_full_validation.pdf.gz | 738.2 KB | Display | |
Data in XML | 5acj_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 5acj_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/5acj ftp://data.pdbj.org/pub/pdb/validation_reports/ac/5acj | HTTPS FTP |
-Related structure data
Related structure data | 5acfC 5acgC 5achC 5aciC 4eirS 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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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*PLUS |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotriose |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 409 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 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.55 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 3.0M SODIUM CHLORIDE, 100MM CITRIC ACID PH3.5, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03841 |
Detector | Type: MARRESEARCH / Detector: CCD |
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: 1.7→30 Å / Num. obs: 35016 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 34.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.67 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 6.16 / % possible all: 98.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EIR Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.244 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.278 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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