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- PDB-6qub: Truncated beta-galactosidase III from Bifidobacterium bifidum in ... -

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Basic information

Entry
Database: PDB / ID: 6qub
TitleTruncated beta-galactosidase III from Bifidobacterium bifidum in complex with galactose
Components(Beta-galactosidase) x 2
KeywordsSUGAR BINDING PROTEIN / TIM BARREL / GLYCOSIDE HYDROLASE / HYDROLASE
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
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) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel 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) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Beta-galactosidase
Similarity search - Component
Biological speciesBifidobacterium bifidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsThirup, S.S. / Nielsen, J.A. / Andersen, J.L. / Alsarraf, H. / Blaise, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Agency for Science Technology and Innovation Denmark
CitationJournal: To Be Published
Title: Truncated beta-galactosidase III from Bifidobacterium bifidum
Authors: Nielsen, J.A. / Andersen, J.L. / Alsarraf, H. / Blaise, M. / Thirup, S.S. / Larsen, M.K. / Cramer, J.F.
History
DepositionFeb 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / refine / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2May 15, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,3028
Polymers187,7822
Non-polymers5216
Water46,0102554
1
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6194
Polymers95,3591
Non-polymers2603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6834
Polymers92,4231
Non-polymers2603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.781, 54.592, 143.357
Angle α, β, γ (deg.)90.00, 107.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-galactosidase


Mass: 95358.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q9F4D5, beta-galactosidase
#2: Protein Beta-galactosidase


Mass: 92422.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q9F4D5, beta-galactosidase
#3: 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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2554 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 23% PEG1500 10mM galactose 10 mM Tris:HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972423 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972423 Å / Relative weight: 1
ReflectionResolution: 1.95→34.2 Å / Num. obs: 119733 / % possible obs: 98 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.617 / Num. unique obs: 12079 / CC1/2: 0.868 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→34.139 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 1871 1.56 %
Rwork0.1688 --
obs0.1695 119684 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→34.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13034 0 28 2554 15616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413412
X-RAY DIFFRACTIONf_angle_d0.74218269
X-RAY DIFFRACTIONf_dihedral_angle_d15.5864725
X-RAY DIFFRACTIONf_chiral_restr0.052019
X-RAY DIFFRACTIONf_plane_restr0.0042375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00270.25731450.20729080X-RAY DIFFRACTION100
2.0027-2.06170.25861430.19449051X-RAY DIFFRACTION99
2.0617-2.12820.26051470.18799191X-RAY DIFFRACTION100
2.1282-2.20430.24871440.19019106X-RAY DIFFRACTION100
2.2043-2.29250.40111210.33487703X-RAY DIFFRACTION84
2.2925-2.39680.26081460.18759145X-RAY DIFFRACTION100
2.3968-2.52310.22221450.17849150X-RAY DIFFRACTION100
2.5231-2.68110.20441450.16649135X-RAY DIFFRACTION99
2.6811-2.88810.22661470.16219232X-RAY DIFFRACTION100
2.8881-3.17850.18791450.15679190X-RAY DIFFRACTION100
3.1785-3.6380.20081460.14529188X-RAY DIFFRACTION99
3.638-4.58170.16451470.13359217X-RAY DIFFRACTION99
4.5817-34.14450.15021500.12769425X-RAY DIFFRACTION99

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