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- PDB-4e8c: Crystal structure of streptococcal beta-galactosidase in complex ... -

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Basic information

Entry
Database: PDB / ID: 4e8c
TitleCrystal structure of streptococcal beta-galactosidase in complex with galactose
ComponentsGlycosyl hydrolase, family 35
KeywordsHYDROLASE / TIM barrel / Beta-Propeller / glycohydrolase
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Glycosyl hydrolase, family 35 / Glycosyl hydrolase, family 35
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCheng, W. / Wang, L. / Bai, X.H. / Jiang, Y.L. / Li, Q. / Yu, G. / Zhou, C.Z. / Chen, Y.X.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural insights into the substrate specificity of Streptococcus pneumoniae beta (1,3)-galactosidase BgaC
Authors: Cheng, W. / Wang, L. / Jiang, Y.L. / Bai, X.H. / Chu, J. / Li, Q. / Yu, G. / Liang, Q.L. / Zhou, C.Z. / Chen, Y.X.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase, family 35
B: Glycosyl hydrolase, family 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,78219
Polymers138,0402
Non-polymers1,74217
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-10 kcal/mol
Surface area41380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.351, 82.374, 99.596
Angle α, β, γ (deg.)90.00, 106.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycosyl hydrolase, family 35 / beta-galactosidase


Mass: 69019.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0060 / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q97T90, UniProt: A0A0H2UN19*PLUS, beta-galactosidase
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.29 Å3/Da / Density % sol: 46.18 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 91359 / Num. obs: 88435 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.04 Å2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 13.3 / Num. unique all: 88435 / Rsym value: 0.062 / % possible all: 96.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E8D

4e8d


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4395 5 %RANDOM
Rwork0.2049 83546 --
obs0.2068 87941 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.01 Å2 / Biso mean: 40.5586 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--4.85 Å20 Å2-1.83 Å2
2--7.39 Å20 Å2
3----3.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9688 0 114 592 10394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210069
X-RAY DIFFRACTIONr_angle_refined_deg0.9411.96513619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5651185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87524.141512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.195151685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2551556
X-RAY DIFFRACTIONr_chiral_restr0.0640.21395
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217766
X-RAY DIFFRACTIONr_mcbond_it2.9851.55884
X-RAY DIFFRACTIONr_mcangle_it3.92829471
X-RAY DIFFRACTIONr_scbond_it3.34434185
X-RAY DIFFRACTIONr_scangle_it4.5754.54146
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 306 -
Rwork0.279 5592 -
all-5898 -
obs--88.61 %

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