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- PDB-1xc6: Native Structure Of Beta-Galactosidase from Penicillium sp. in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xc6 | |||||||||
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Title | Native Structure Of Beta-Galactosidase from Penicillium sp. in complex with Galactose | |||||||||
![]() | Beta-Galactosidase | |||||||||
![]() | HYDROLASE / Tim Barrel Domain / Glycoside Hydrolase / Family GH35 / Glycoprotein / Penicillium / Quick Cryo Soaking | |||||||||
Function / homology | ![]() galactose binding / lactose catabolic process / beta-galactosidase / vacuole / beta-galactosidase activity / polysaccharide catabolic process / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rojas, A.L. / Nagem, R.A.P. / Neustroev, K.N. / Arand, M. / Adamska, M. / Eneyskaya, E.V. / Kulminskaya, A.A. / Garratt, R.C. / Golubev, A.M. / Polikarpov, I. | |||||||||
![]() | ![]() Title: Crystal Structures of beta-Galactosidase from Penicillium sp. and its Complex with Galactose Authors: Rojas, A.L. / Nagem, R.A.P. / Neustroev, K.N. / Arand, M. / Adamska, M. / Eneyskaya, E.V. / Kulminskaya, A.A. / Garratt, R.C. / Golubev, A.M. / Polikarpov, I. #1: ![]() Title: purification, crystallization and preliminary diffraction study of beta-galactosidase from Penicillium sp. Authors: Neustroev, K.N. / De Sousa, E.A. / Golubev, A.M. / Brandao Neto, J.R. / Eneyskaya, E.V. / Kulminskaya, A.A. / Polikarpov, I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.9 KB | Display | ![]() |
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PDB format | ![]() | 184.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 46.7 KB | Display | |
Data in CIF | ![]() | 72.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 monomer in the asymetric unit. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 105683.844 Da / Num. of mol.: 1 / Fragment: mature peptide (residues 41-1011) / Source method: isolated from a natural source / Source: (natural) ![]() References: GenBank: 44844271, UniProt: Q700S9*PLUS, beta-galactosidase |
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-Sugars , 7 types, 8 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#2: 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 | ||
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#3: 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-(1-3)]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 | ||
#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: 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 | ||
#6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[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 | ||
#7: Sugar | #8: Sugar | ChemComp-GAL / | |
-Non-polymers , 5 types, 1017 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#9: Chemical | ChemComp-NA / | ||||
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#10: Chemical | ChemComp-PO4 / | ||||
#11: Chemical | ChemComp-IOD / #12: Chemical | ChemComp-EDO / #13: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 15% PEG 8000, 50 MM Sodium Phosphate (Iodide ions were incorporated into the crystal by Quick Cryo Soaking technique at room temperature), pH 4.0, Vapor Diffusion, Hanging Drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→23.4 Å / Num. all: 224036 / Num. obs: 224036 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 22.63 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→23.4 Å
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Refine LS restraints |
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