+Open data
-Basic information
Entry | Database: PDB / ID: 1tg7 | |||||||||
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Title | Native structure of beta-galactosidase from Penicillium sp. | |||||||||
Components | beta-galactosidase | |||||||||
Keywords | HYDROLASE / TIM barrel domain / glycoside hydrolase / family GH35 / glycoprotein / Penicillium | |||||||||
Function / homology | Function and homology information lactose catabolic process / galactose binding / beta-galactosidase / beta-galactosidase activity / polysaccharide catabolic process / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | Penicillium sp. (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 Å | |||||||||
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. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 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: Journal: Acta Crystallogr.,Sect.D / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tg7.cif.gz | 237.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tg7.ent.gz | 188.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/1tg7 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/1tg7 | 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. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 105683.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium sp. (fungus) References: GenBank: 44844271, UniProt: Q700S9*PLUS, beta-galactosidase |
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-Sugars , 6 types, 7 molecules
#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 |
-Non-polymers , 4 types, 1268 molecules
#8: Chemical | #9: Chemical | ChemComp-PO4 / #10: Chemical | ChemComp-EDO / #11: Water | ChemComp-HOH / | |
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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: 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, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.54 Å |
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: 1.9→22.3 Å / Num. all: 155025 / Num. obs: 152744 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.9→22.3 Å / σ(F): 0 / σ(I): 3.2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→22.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015
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