+Open data
-Basic information
Entry | Database: PDB / ID: 5nln | |||||||||
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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: 1.9 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 | 5nln.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nln.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nln_validation.pdf.gz | 771.3 KB | Display | wwPDB validaton report |
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Full document | 5nln_full_validation.pdf.gz | 772.4 KB | Display | |
Data in XML | 5nln_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 5nln_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/5nln ftp://data.pdbj.org/pub/pdb/validation_reports/nl/5nln | HTTPS FTP |
-Related structure data
Related structure data | 5nkwC 5nloC 5nlpC 5nlqC 5nlrC 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) / Strain (production host): MT3568 / References: UniProt: A0A0S2GKZ1 |
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-Sugars , 3 types, 5 molecules
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose |
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#4: Sugar | ChemComp-NAG / |
#6: Sugar |
-Non-polymers , 3 types, 410 molecules
#3: Chemical | ChemComp-CU / | ||
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#5: Chemical | ChemComp-CL / #7: 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: 3.24 Å3/Da / Density % sol: 62.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 3.6M NaCl 0.1 M citric acid pH4.5 (soaked in pH5.5) PH range: 4.5-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 27034 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.67 % / CC1/2: 0.988 / Rrim(I) all: 0.289 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 8.84 % / Num. unique obs: 1914 / CC1/2: 0.625 / Rrim(I) all: 1.58 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ACH Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.394 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.119 / 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: 19.634 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50 Å
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Refine LS restraints |
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