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- PDB-2pbg: 6-PHOSPHO-BETA-D-GALACTOSIDASE FORM-B -

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Basic information

Entry
Database: PDB / ID: 2pbg
Title6-PHOSPHO-BETA-D-GALACTOSIDASE FORM-B
Components6-PHOSPHO-BETA-D-GALACTOSIDASE
KeywordsHYDROLASE / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / lactose catabolic process via tagatose-6-phosphate / beta-glucosidase activity / cytosol
Similarity search - Function
6-phospho-beta-galactosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...6-phospho-beta-galactosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-phospho-beta-galactosidase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWiesmann, 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
DepositionFeb 21, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-PHOSPHO-BETA-D-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2512
Polymers54,1551
Non-polymers961
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.000, 179.600, 60.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 6-PHOSPHO-BETA-D-GALACTOSIDASE / PGAL


Mass: 54155.176 Da / Num. of mol.: 1 / Mutation: S256C
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURES HAVE BEEN ASSIGNED BY THE PROGRAM DSSP. THERE ARE SOME DISCREPANCIES WITH ...THE SECONDARY STRUCTURES HAVE BEEN ASSIGNED BY THE PROGRAM DSSP. THERE ARE SOME DISCREPANCIES WITH THE PUBLICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
20.1 M1dropKH2PO4
30.02 %1dropNaN3
428 %PEG40001reservoir
50.2 M1reservoirLi2SO4
60.1 MTris-HCl1reservoir
70.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→1000 Å / Num. obs: 16050 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.096
Reflection shellResolution: 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

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
BIOMOLdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PBG

1pbg


Resolution: 2.5→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.295 -RANDOM
Rwork0.182 --
obs0.182 15442 -
Displacement parametersBiso mean: 10.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati sigma a obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 5 160 4001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.31
X-RAY DIFFRACTIONx_mcangle_it3.81
X-RAY DIFFRACTIONx_scbond_it3.08
X-RAY DIFFRACTIONx_scangle_it4.34
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.294
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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