[English] 日本語
Yorodumi- PDB-4iug: Crystal structure of beta-galactosidase from Aspergillus oryzae i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iug | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of beta-galactosidase from Aspergillus oryzae in complex with galactose | |||||||||
Components | Beta-galactosidase A | |||||||||
Keywords | HYDROLASE / Tim Barrel / Glycoside hydrolase | |||||||||
Function / homology | Function and homology information galactose binding / lactose catabolic process / beta-galactosidase / beta-galactosidase activity / polysaccharide catabolic process / extracellular space Similarity search - Function | |||||||||
Biological species | Aspergillus oryzae (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Maksimainen, M. / Rouvinen, J. | |||||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2013 Title: The crystal structure of acidic beta-galactosidase from Aspergillus oryzae. Authors: Maksimainen, M.M. / Lampio, A. / Mertanen, M. / Turunen, O. / Rouvinen, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4iug.cif.gz | 218 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4iug.ent.gz | 172.1 KB | Display | PDB format |
PDBx/mmJSON format | 4iug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iug_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4iug_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4iug_validation.xml.gz | 39.5 KB | Display | |
Data in CIF | 4iug_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/4iug ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iug | HTTPS FTP |
-Related structure data
Related structure data | 1tg7S S: Starting model for refinement |
---|---|
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: 110052.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: lacA / Production host: Kluyveromyces lactis (yeast) / References: UniProt: Q2UCU3, beta-galactosidase |
---|
-Sugars , 7 types, 8 molecules
#2: 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 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...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 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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 #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-6-O-phosphono-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-GAL / | #9: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 309 molecules
#7: Chemical | ChemComp-CD / #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.89 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M cadmium chloride, 0.1 M sodium acetate, 30 % (w/v) PEG 400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2012 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.914 Å / Num. obs: 52147 / % possible obs: 99.8 % / Observed criterion σ(I): 3.11 |
Reflection shell | Resolution: 2.6→2.7 Å / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TG7 Resolution: 2.6→47.914 Å / SU ML: 0.35 / σ(F): 2 / Phase error: 20.26 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.653 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→47.914 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|