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- PDB-4ucf: Crystal structure of Bifidobacterium bifidum beta-galactosidase i... -

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Basic information

Entry
Database: PDB / ID: 4ucf
TitleCrystal structure of Bifidobacterium bifidum beta-galactosidase in complex with alpha-galactose
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / LACTASE / FAMILY 42
Function / homology
Function and homology information


galactose metabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity
Similarity search - Function
Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II ...Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-D-galactopyranose / DI(HYDROXYETHYL)ETHER / N-PROPANOL / Beta-galactosidase
Similarity search - Component
Biological speciesBIFIDOBACTERIUM BIFIDUM S17 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsGodoy, A.S. / Murakami, M.T. / Camilo, C.M. / Bernardes, A. / Polikarpov, I.
CitationJournal: FEBS J. / Year: 2016
Title: Crystal Structure of Beta1-6-Galactosidase from Bifidobacterium Bifidum S17: Trimeric Architecture, Molecular Determinants of the Enzymatic Activity and its Inhibition by Alpha-Galactose.
Authors: Godoy, A.S. / Camilo, C.M. / Kadowaki, M.A. / Muniz, H.D. / Santo, M.E. / Murakami, M.T. / Nascimento, A.S. / Polikarpov, I.
History
DepositionDec 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 2.0Aug 23, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_source ...atom_site / diffrn_source / pdbx_distant_solvent_atoms / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _diffrn_source.type / _pdbx_distant_solvent_atoms.auth_asym_id ..._diffrn_source.type / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.3Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: BETA-GALACTOSIDASE
B: BETA-GALACTOSIDASE
C: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,26212
Polymers231,8353
Non-polymers1,4279
Water36,4082021
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18480 Å2
ΔGint-55.9 kcal/mol
Surface area61610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.720, 101.592, 114.625
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-GALACTOSIDASE / BETA-GAL


Mass: 77278.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BIFIDOBACTERIUM BIFIDUM S17 (bacteria)
Description: COURTESY OF PROF. CHRISTIAN RIEDEL, ULM UNIVERSITY, GERMANY
Plasmid: PPROEX HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E3EPA1, beta-galactosidase
#2: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2021 / 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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: NONE
Crystal growTemperature: 292 K / pH: 6
Details: 20% (W/V) POLYETHYLENE GLYCOL 3, 350, 0.2 M DIBASIC AMMONIUM TARTRATE AND 4% (W/V) 1-PROPANOL AT 292 K, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→42.8 Å / Num. obs: 153059 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.8.007refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UZS

4uzs


Resolution: 1.94→110.51 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.36 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDECHAINS WERE REMOVED FROM MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.20606 7688 5 %RANDOM
Rwork0.15505 ---
obs0.15762 145369 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.194 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å21.06 Å2
2---1.98 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.94→110.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16138 0 95 2021 18254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01916709
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215041
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.93122763
X-RAY DIFFRACTIONr_angle_other_deg0.909334549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5852054
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17923.504819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.759152508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.93315122
X-RAY DIFFRACTIONr_chiral_restr0.1080.22400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02119172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024040
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_it1.8432.3598210
X-RAY DIFFRACTIONr_mcbond_other1.8372.3598209
X-RAY DIFFRACTIONr_mcangle_it2.5773.52810254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.52.5468499
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: 1.941→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 496 -
Rwork0.245 8936 -
obs--81.17 %

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