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- PDB-4cu6: Unravelling the multiple functions of the architecturally intrica... -

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Basic information

Entry
Database: PDB / ID: 4cu6
TitleUnravelling the multiple functions of the architecturally intricate Streptococcus pneumoniae beta-galactosidase, BgaA
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / carbohydrate catabolic process / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Beta-galactosidase-like, Galactose-binding domain / Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / G5 domain ...: / Beta-galactosidase-like, Galactose-binding domain / Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / G5 domain / G5 domain / G5 domain profile. / G5 / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-galactosidase / Beta-galactosidase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSingh, A.K. / Pluvinage, B. / Higgins, M.A. / Dalia, A.B. / Flynn, M. / Lloyd, A.R. / Weiser, J.N. / Stubbs, K.A. / Boraston, A.B. / King, S.J.
CitationJournal: Plos Pathog. / Year: 2014
Title: Unravelling the Multiple Functions of the Architecturally Intricate Streptococcus Pneumoniae Beta-Galactosidase, Bgaa.
Authors: Singh, A.K. / Pluvinage, B. / Higgins, M.A. / Dalia, A.B. / Woodiga, S.A. / Flynn, M. / Lloyd, A.R. / Weiser, J.N. / Stubbs, K.A. / Boraston, A.B. / King, S.J.
History
DepositionMar 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2May 8, 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.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,22645
Polymers96,3251
Non-polymers2,90144
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.770, 116.770, 220.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-3442-

HOH

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Components

#1: Protein BETA-GALACTOSIDASE / GLYCOSIDE HYDROLASE 2


Mass: 96325.125 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 137-985
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE TIGR4 (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: I6L8R4, UniProt: A0A0H2UP19*PLUS, beta-galactosidase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O

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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: 3.89 Å3/Da / Density % sol: 68.41 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→19.94 Å / Num. obs: 42431 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→116.77 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.433 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22126 2139 5 %RANDOM
Rwork0.1781 ---
obs0.18031 40273 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.162 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.7→116.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6760 0 181 492 7433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197115
X-RAY DIFFRACTIONr_bond_other_d0.0010.026606
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.949569
X-RAY DIFFRACTIONr_angle_other_deg2.377315161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25824.404361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.082151166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5321542
X-RAY DIFFRACTIONr_chiral_restr0.080.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028121
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021711
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1522.3223417
X-RAY DIFFRACTIONr_mcbond_other1.1532.323416
X-RAY DIFFRACTIONr_mcangle_it1.9543.4794280
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6422.4883698
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 169 -
Rwork0.269 2924 -
obs--99.97 %

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