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Yorodumi- PDB-5fjj: Three-dimensional structures of two heavily N-glycosylated Asperg... -
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-Basic information
Entry | Database: PDB / ID: 5fjj | |||||||||
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Title | Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. Family GH3 beta-D-glucosidases | |||||||||
Components | BETA-GLUCOSIDASE | |||||||||
Keywords | HYDROLASE / N-GLYCOSYLATION / GLUCOSIDASE | |||||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase / carbohydrate catabolic process / beta-glucosidase activity / cellulose catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | ASPERGILLUS ORYZAE (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Agirre, J. / Ariza, A. / Offen, W.A. / Turkenburg, J.P. / Roberts, S.M. / McNicholas, S. / Harris, P.V. / McBrayer, B. / Dohnalek, J. / Cowtan, K.D. ...Agirre, J. / Ariza, A. / Offen, W.A. / Turkenburg, J.P. / Roberts, S.M. / McNicholas, S. / Harris, P.V. / McBrayer, B. / Dohnalek, J. / Cowtan, K.D. / Davies, G.J. / Wilson, K.S. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2016 Title: Three-Dimensional Structures of Two Heavily N-Glycosylated Aspergillus Sp. Family Gh3 Beta-D-Glucosidases Authors: Agirre, J. / Ariza, A. / Offen, W.A. / Turkenburg, J.P. / Roberts, S.M. / Mcnicholas, S. / Harris, P.V. / Mcbrayer, B. / Dohnalek, J. / Cowtan, K.D. / Davies, G.J. / Wilson, K.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fjj.cif.gz | 744 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fjj.ent.gz | 611.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/5fjj ftp://data.pdbj.org/pub/pdb/validation_reports/fj/5fjj | HTTPS FTP |
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-Related structure data
Related structure data | 5fjiSC 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 91626.266 Da / Num. of mol.: 4 / Fragment: MATURE PROTEIN, RESIDUES 20-861 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS ORYZAE (mold) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q2UUD6, beta-glucosidase |
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-Sugars , 14 types, 38 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-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 #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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 #9: 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)-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 #10: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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 #11: 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 #12: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 #13: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 #14: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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 #15: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 2120 molecules
#16: Chemical | ChemComp-PEG / #17: Chemical | ChemComp-MG / #18: Chemical | ChemComp-PO4 / | #19: Chemical | ChemComp-CL / #20: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE FIRST 19 AMINO ACIDS ARE A PREDICTED SIGNAL PEPTIDE AND ARE THEREFORE NOT PRESENT IN THE MATURE PROTEIN. |
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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | Details: 0.1M HEPES PH 7.5, 0.2M MAGNESIUM CHLORIDE, 30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 8, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→88.23 Å / Num. obs: 271085 / % possible obs: 98.4 % / Observed criterion σ(I): 1.9 / Redundancy: 6.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.9 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FJI Resolution: 1.95→114.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.933 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 20-22 ARE NOT VISIBLE FOR ALL 4 CHAINS, AND RESIDUE 861 IS DISORDERED IN MOLECULES B AND D. MODELED SUGARS WERE CHECKED USING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 20-22 ARE NOT VISIBLE FOR ALL 4 CHAINS, AND RESIDUE 861 IS DISORDERED IN MOLECULES B AND D. MODELED SUGARS WERE CHECKED USING PRIVATEER. THERE ARE REGIONS OF UNMODELLED DENSITY ASSOCIATED WITH SUGAR CHAINS IN THE FOLLOWING. FOR CHAIN A, NEAR O3 BMA1103 O4 MAN1106 O3 BMA 1203 O3 BMA 1503 O3 1504 O6 MAN 1704. FOR CHAIN B, NEAR O3 BMA 1003 O3 MAN1004 O2 MAN 1105 O3 BMA 1203 O3 BMA 1503 O3 BMA 1703 O6 MAN 1704 O2 MAN 1705. FOR CHAIN C, NEAR O3 BMA 1003 O6 BMA 1103 O2 MAN 1105 O6 BMA 1203 O2 MAN 1304 O3 BMA 1503 O4 NAG 1802. FOR CHAIN D, O3 BMA 1303 O3 BMA 1503 O6 MAN 1704 O4 NAG 1801.
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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: 30.507 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→114.43 Å
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Refine LS restraints |
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