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- PDB-1pbg: THE THREE-DIMENSIONAL STRUCTURE OF 6-PHOSPHO-BETA GALACTOSIDASE F... -

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Basic information

Entry
Database: PDB / ID: 1pbg
TitleTHE THREE-DIMENSIONAL STRUCTURE OF 6-PHOSPHO-BETA GALACTOSIDASE FROM LACTOCOCCUS LACTIS
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
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 / Resolution: 2.3 Å
AuthorsWiesmann, C. / Schulz, G.E.
Citation
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.
#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: 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
DepositionSep 14, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,4704
Polymers108,2782
Non-polymers1922
Water7,494416
1
A: 6-PHOSPHO-BETA-D-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2352
Polymers54,1391
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 6-PHOSPHO-BETA-D-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2352
Polymers54,1391
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.500, 83.200, 105.700
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 48 / 2: CIS PROLINE - PRO A 176 / 3: TRP A 421 - SER A 422 IS A CIS PEPTIDE. / 4: CIS PROLINE - PRO B 48 / 5: CIS PROLINE - PRO B 176 / 6: TRP B 421 - SER B 422 IS A CIS PEPTIDE.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999948, -0.00719, 0.00717), (-0.010128, -0.756585, 0.653816), (0.000724, -0.653855, -0.756619)
Vector: 39.7384, -32.8843, 108.8566)

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Components

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


Mass: 54139.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PRECIPITANT POLYETHYLENE GLYCOL
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: SUBSP. LACTIS 712 / Description: DELTA H DELTA 1TRP / Gene: LACG / Plasmid: PNZ316 / Gene (production host): LACG / Production host: Escherichia coli (E. coli) / References: UniProt: P11546, 6-phospho-beta-galactosidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE ASSIGNMENT WAS DONE BY THE PROGRAM DSSP. FOR A MANUAL ASSIGNMENT CHECK THE MOST ...SECONDARY STRUCTURE ASSIGNMENT WAS DONE BY THE PROGRAM DSSP. FOR A MANUAL ASSIGNMENT CHECK THE MOST RECENT 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
126-30 %PEG40001reservoir
20.1 MTris-HCl1reservoir
30.2 M1reservoirLi2SO4
40.02 %1reservoirNaN3

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 36765 / % possible obs: 78.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.236 -5 %
Rwork0.164 --
obs0.164 36241 78.7 %
Displacement parametersBiso mean: 19.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7472 0 10 416 7898
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.52
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.51.5
X-RAY DIFFRACTIONx_mcangle_it4.92
X-RAY DIFFRACTIONx_scbond_it5.42
X-RAY DIFFRACTIONx_scangle_it7.72.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24

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