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Yorodumi- PDB-5nbs: Structural studies of a Glycoside Hydrolase Family 3 beta-glucosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nbs | |||||||||
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Title | Structural studies of a Glycoside Hydrolase Family 3 beta-glucosidase from the Model Fungus Neurospora crassa | |||||||||
Components | Beta-glucosidase | |||||||||
Keywords | HYDROLASE / Glycoside hydrolase / beta-glucosidase / Biodegradation / Neurospora crassa | |||||||||
Function / homology | Function and homology information glucan catabolic process / scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | Neurospora crassa OR74A (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Gudmundsson, M. / Karkehabadi, S. / Kaper, T. / Sandgren, M. | |||||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Structural studies of a glycoside hydrolase family 3 beta-glucosidase from the model fungus Neurospora crassa. Authors: Karkehabadi, S. / Hansson, H. / Mikkelsen, N.E. / Kim, S. / Kaper, T. / Sandgren, M. / Gudmundsson, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nbs.cif.gz | 707.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nbs.ent.gz | 592.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nbs ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nbs | HTTPS FTP |
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-Related structure data
Related structure data | 4iibS S: Starting model for refinement |
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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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Unit cell |
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-Components
-Protein / Non-polymers , 2 types, 956 molecules AB
#10: Water | ChemComp-HOH / |
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#1: Protein | Mass: 93908.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa OR74A (fungus) / Gene: gh3-3, NCU08755 / Production host: Trichoderma reesei RUT C-30 (fungus) / References: UniProt: Q7RWP2, beta-glucosidase |
-Sugars , 8 types, 22 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
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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: 5.1 Å3/Da / Density % sol: 61 % / Description: Rhomboidal sheets |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.2 M ammonium citrate dibasic at pH 5.1 and 20 % w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2013 |
Radiation | Monochromator: Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→47 Å / Num. obs: 113592 / % possible obs: 99.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.028 / Rrim(I) all: 0.04 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.25→2.308 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 7878 / CC1/2: 0.825 / Rpim(I) all: 0.38 / Rrim(I) all: 0.53 / % possible all: 99.15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IIB Resolution: 2.25→47 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.943 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.189 / 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: 34.929 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→47 Å
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