+Open data
-Basic information
Entry | Database: PDB / ID: 4pbg | ||||||
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Title | 6-PHOSPHO-BETA-GALACTOSIDASE FORM-CST | ||||||
Components | 6-PHOSPHO-BETA-D-GALACTOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE | ||||||
Function / homology | Function and homology information 6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / lactose catabolic process via tagatose-6-phosphate Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wiesmann, C. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis. Authors: Wiesmann, C. / Hengstenberg, W. / Schulz, G.E. #1: Journal: Eur.J.Biochem. / Year: 1995 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: Journal: Structure / Year: 1995 Title: The Three-Dimensional Structure of 6-Phospho-Beta-Galactosidase from Lactococcus Lactis Authors: Wiesmann, C. / Beste, G. / Hengstenberg, W. / Schulz, G.E. #3: Journal: Protein Eng. / Year: 1993 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pbg.cif.gz | 203.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pbg.ent.gz | 163.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pbg_validation.pdf.gz | 930 KB | Display | wwPDB validaton report |
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Full document | 4pbg_full_validation.pdf.gz | 950.1 KB | Display | |
Data in XML | 4pbg_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 4pbg_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/4pbg ftp://data.pdbj.org/pub/pdb/validation_reports/pb/4pbg | HTTPS FTP |
-Related structure data
Related structure data | 2pbgC 3pbgC 1pbgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99987, 0.01597, 0.00069), Vector: |
-Components
#1: Protein | Mass: 54113.141 Da / Num. of mol.: 2 / Mutation: G375C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Strain: SUBSP. LACTIS 712 / Gene: LACG / Plasmid: PNZ316 / Gene (production host): LACG / Production host: Escherichia coli (E. coli) / Strain (production host): DELTA H1 DELTA TRP / References: UniProt: P11546, 6-phospho-beta-galactosidase #2: Sugar | #3: Water | ChemComp-HOH / | Compound details | THE SECONDARY STRUCTURES HAVE BEEN ASSIGNED BY THE PROGRAM DSSP. THERE ARE SOME DISCREPANCIES WITH ...THE SECONDARY STRUCTURES | |
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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: 2.7 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: PEG-4000, PH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1995 |
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: 35989 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.09 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 32734 / Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PBG Resolution: 2.5→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / σ(F): 0
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Displacement parameters | Biso mean: 14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati sigma a obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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