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- PDB-5ihr: STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN C... -

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Basic information

Entry
Database: PDB / ID: 5ihr
TitleSTRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH ALLOLACTOSE
ComponentsProbable beta-galactosidase A
KeywordsHYDROLASE / TIM barrel / GH35 / GLYCOSIDE HYDROLASE / KINETICS / PROTEIN CONFORMATION / carbohydrate metabolism / b-galactosidase / Aspergillus niger / fungal protein / SUBSTRATE SPECIFICITY / prebiotics / galactooligosaccharides / GOS / recombinant / allolactose / b-D-galactopyranosyl-(1-6)-D-glucopyranose
Function / homology
Function and homology information


oligosaccharide binding / lactose catabolic process / beta-galactosidase / beta-galactosidase activity / polysaccharide catabolic process / carbohydrate metabolic process / extracellular region
Similarity search - Function
beta-galactosidase, domain 2 / Beta-galactosidase, domain 2 / beta-galactosidase, domain 3 / Beta-galactosidase, domain 3 / Beta-galactosidase, domain 3 / Beta-galactosidase, domain 3 superfamily / Beta-galactosidase, domain 3 / Beta-galactosidase jelly roll domain / Beta-galactosidase, domain 2 / Beta-galactosidase, domain 2 superfamily ...beta-galactosidase, domain 2 / Beta-galactosidase, domain 2 / beta-galactosidase, domain 3 / Beta-galactosidase, domain 3 / Beta-galactosidase, domain 3 / Beta-galactosidase, domain 3 superfamily / Beta-galactosidase, domain 3 / Beta-galactosidase jelly roll domain / Beta-galactosidase, domain 2 / Beta-galactosidase, domain 2 superfamily / Beta-galactosidase, domain 2 / Beta-galactosidase, domain 2 / Beta-galactosidase second all-beta domain / Glycoside hydrolase, family 35, conserved site / Glycosyl hydrolases family 35 putative active site. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / 3-layer Sandwich / 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-galactosidase A
Similarity search - Component
Biological speciesAspergillus niger CBS 513.88 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRico-Diaz, A. / Ramirez-Escudero, M. / Vizoso Vazquez, A. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J.
CitationJournal: FEBS J. / Year: 2017
Title: Structural features of Aspergillus niger beta-galactosidase define its activity against glycoside linkages.
Authors: Rico-Diaz, A. / Ramirez-Escudero, M. / Vizoso-Vazquez, A. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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.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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable beta-galactosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,00022
Polymers110,6281
Non-polymers6,37221
Water4,792266
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint126 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.144, 111.406, 125.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable beta-galactosidase A / Lactase A


Mass: 110627.859 Da / Num. of mol.: 1 / Mutation: E298Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger CBS 513.88 (mold) / Gene: lacA, An01g12150 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ3505 / References: UniProt: A2QAN3, beta-galactosidase

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Sugars , 4 types, 10 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-galactopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][b-D-Galp]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 277 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.54 % / Description: Rod-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 23% (W/V) PEG 3350, 0.1M BIS-TRIS BUFFER PH 5.5 , 0.2M LITHIUM SULPHATE, then soaked in 30 mM allolactose
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97872 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2015 / Details: kbmirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→83.42 Å / Num. obs: 47163 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.138 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimless0.5.21data scaling
MOLREP11.4.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFP

5ifp


Resolution: 2.4→83.42 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.844 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.21 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20044 2364 5 %RANDOM
Rwork0.16244 ---
obs0.16432 44754 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.699 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å2-0 Å2
2--0.47 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 2.4→83.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7483 0 409 266 8158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028115
X-RAY DIFFRACTIONr_bond_other_d0.0010.027283
X-RAY DIFFRACTIONr_angle_refined_deg1.2112.0111103
X-RAY DIFFRACTIONr_angle_other_deg0.707316732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585967
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22924.527338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.311151159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0281527
X-RAY DIFFRACTIONr_chiral_restr0.0630.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021792
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_it0.8652.0593871
X-RAY DIFFRACTIONr_mcbond_other0.8652.0583870
X-RAY DIFFRACTIONr_mcangle_it1.5133.0854837
X-RAY DIFFRACTIONr_mcangle_other1.5143.0864838
X-RAY DIFFRACTIONr_scbond_it1.2122.3294244
X-RAY DIFFRACTIONr_scbond_other1.2112.3294241
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0313.4326261
X-RAY DIFFRACTIONr_long_range_B_refined3.37516.869056
X-RAY DIFFRACTIONr_long_range_B_other3.37516.8669057
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 182 -
Rwork0.209 3286 -
obs--99.86 %

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