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- PDB-3og2: Native crystal structure of Trichoderma reesei beta-galactosidase -
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Open data
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Basic information
Entry | Database: PDB / ID: 3og2 | |||||||||
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Title | Native crystal structure of Trichoderma reesei beta-galactosidase | |||||||||
![]() | Beta-galactosidase | |||||||||
![]() | HYDROLASE / TIM barrel domain / Glycoside hydrolase / Family 35 / Glycoprotein | |||||||||
Function / homology | ![]() beta-galactosidase / beta-galactosidase activity / vacuole / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Maksimainen, M. / Rouvinen, J. | |||||||||
![]() | ![]() Title: Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site Authors: Maksimainen, M. / Hakulinen, N. / Kallio, J.M. / Timoharju, T. / Turunen, O. / Rouvinen, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 452.3 KB | Display | ![]() |
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PDB format | ![]() | 363.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ogrC ![]() 3ogsC ![]() 3ogvC ![]() 1tg7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 109395.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 4 types, 5 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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 |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 |
#4: 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 |
#5: Sugar |
-Non-polymers , 2 types, 995 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 8% PEG 8000, 0.1M sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 376588 / Num. obs: 341073 / % possible obs: 90.6 % / Observed criterion σ(I): 3.28 |
Reflection shell | Resolution: 1.2→1.3 Å / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TG7 Resolution: 1.2→20 Å / Num. parameters: 81499 / Num. restraintsaints: 96685 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 27 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 8904 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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