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Yorodumi- PDB-1y4w: Crystal structure of exo-inulinase from Aspergillus awamori in sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y4w | |||||||||
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Title | Crystal structure of exo-inulinase from Aspergillus awamori in spacegroup P21 | |||||||||
Components | exo-inulinase | |||||||||
Keywords | HYDROLASE / Exo-inulinase / Aspergillus awamori / Glycoside hydrolase family 32 / Crystallographic structure / native structure | |||||||||
Function / homology | Function and homology information fructan beta-fructosidase / fructan beta-fructosidase activity / sucrose alpha-glucosidase activity / sucrose catabolic process / polysaccharide catabolic process / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Aspergillus awamori (mold) | |||||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 1.55 Å | |||||||||
Authors | Nagem, R.A.P. / Rojas, A.L. / Golubev, A.M. / Korneeva, O.S. / Eneyskaya, E.V. / Kulminskaya, A.A. / Neustroev, K.N. / Polikarpov, I. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of exo-inulinase from Aspergillus awamori: the enzyme fold and structural determinants of substrate recognition Authors: Nagem, R.A.P. / Rojas, A.L. / Golubev, A.M. / Korneeva, O.S. / Eneyskaya, E.V. / Kulminskaya, A.A. / Neustroev, K.N. / Polikarpov, I. #1: Journal: BIOCHEM.J. / Year: 2002 Title: Purification, characterization, gene cloning and preliminary X-ray data of the exo-inulinase from Aspergillus awamori Authors: Arand, M. / Golubev, A.M. / Neto, J.R. / Polikarpov, I. / Wattiez, R. / Korneeva, O.S. / Eneyskaya, E.V. / Kulminskaya, A.A. / Shabalin, K.A. / Shishliannikov, S.M. / Chepurnaya, O.V. / Neustroev, K.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y4w.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y4w.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 1y4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/1y4w ftp://data.pdbj.org/pub/pdb/validation_reports/y4/1y4w | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer generated from the structure in the asymmetric unit by the identity operation. |
-Components
#1: Protein | Mass: 57188.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus awamori (mold) / Strain: 2250 References: GenBank: 14787237, UniProt: Q96TU3*PLUS, fructan beta-fructosidase | ||||
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#2: 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 | ||||
#3: Sugar | #4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 15% PEG3350, 1mM sodium cacodylate, 20-100mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2003 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→17.79 Å / Num. all: 86419 / Num. obs: 78641 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.5 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.55→17.79 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.196 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.084 / ESU R Free: 0.084 / 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: 14.911 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→17.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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