+Open data
-Basic information
Entry | Database: PDB / ID: 5nls | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Auxiliary activity 9 | |||||||||
Components | Auxiliary activity 9 | |||||||||
Keywords | OXIDOREDUCTASE / Enzyme | |||||||||
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: 1.75 Å | |||||||||
Authors | Frandsen, K.E.H. / Poulsen, J.-C.N. / Tandrup, T. / Lo Leggio, L. | |||||||||
Funding support | Denmark, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5nls.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5nls.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 5nls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nls_validation.pdf.gz | 696 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5nls_full_validation.pdf.gz | 696.7 KB | Display | |
Data in XML | 5nls_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5nls_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/5nls ftp://data.pdbj.org/pub/pdb/validation_reports/nl/5nls | HTTPS FTP |
-Related structure data
Related structure data | 5nkwC 5nlnC 5nloC 5nlpC 5nlqC 5nlrC 5nltC 5achS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-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 |
---|
-Sugars , 2 types, 2 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose |
---|---|
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 250 molecules
#3: Chemical | ChemComp-CU / | ||||
---|---|---|---|---|---|
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.97 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 3.2 M NaCl 0.1 M citric acid, pH3.5 (soaked in pH 5.5) PH range: 3.5-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 9, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 34937 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 10.36 % / CC1/2: 0.997 / Rrim(I) all: 0.118 / Net I/σ(I): 11.53 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 10.07 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2502 / CC1/2: 0.404 / Rrim(I) all: 1.81 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ACH Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.982 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.736 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|