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Open data
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Basic information
Entry | Database: PDB / ID: 2pbg | ||||||
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Title | 6-PHOSPHO-BETA-D-GALACTOSIDASE FORM-B | ||||||
![]() | 6-PHOSPHO-BETA-D-GALACTOSIDASE | ||||||
![]() | HYDROLASE / GLYCOSYL HYDROLASE | ||||||
Function / homology | ![]() 6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / lactose catabolic process via tagatose-6-phosphate / beta-glucosidase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wiesmann, C. / Schulz, G.E. | ||||||
![]() | ![]() Title: Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis. Authors: Wiesmann, C. / Hengstenberg, W. / Schulz, G.E. #1: ![]() Title: Identification of the Active-Site Nucleophile in 6-Phospho-Beta-Galactosidase from Staphylococcus Aureus by Labelling with Synthetic Inhibitors Authors: Staedtler, P. / Hoenig, S. / Frank, R. / Withers, S.G. / Hengstenberg, W. #2: ![]() Title: The Three-Dimensional Structure of 6-Phospho-Beta-Galactosidase from Lactococcus Lactis Authors: Wiesmann, C. / Beste, G. / Hengstenberg, W. / Schulz, G.E. #3: ![]() Title: 6-Phospho-Beta-Galactosidases of Gram-Positive and 6-Phospho-Beta-Glucosidase B of Gram-Negative Bacteria: Comparison of Structure and Function by Kinetic and Immunological Methods and ...Title: 6-Phospho-Beta-Galactosidases of Gram-Positive and 6-Phospho-Beta-Glucosidase B of Gram-Negative Bacteria: Comparison of Structure and Function by Kinetic and Immunological Methods and Mutagenesis of the Lacg Gene of Staphylococcus Aureus Authors: Witt, E. / Frank, R. / Hengstenberg, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.4 KB | Display | ![]() |
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PDB format | ![]() | 83.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.7 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pbgC ![]() 4pbgC ![]() 1pbgS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 54155.176 Da / Num. of mol.: 1 / Mutation: S256C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SUBSP. LACTIS 712 / Gene: LACG / Plasmid: PNZ316 / Gene (production host): LACG / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Compound details | THE SECONDARY STRUCTURES HAVE BEEN ASSIGNED BY THE PROGRAM DSSP. THERE ARE SOME DISCREPANCIES WITH ...THE SECONDARY STRUCTURES |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→1000 Å / Num. obs: 16050 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.096 |
Reflection shell | Resolution: 2.43→2.5 Å / % possible all: 50 |
Reflection | *PLUS Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 50 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PBG Resolution: 2.5→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 10.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å / Luzzati sigma a obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.294 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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