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- PDB-5mui: Glycoside hydrolase BT_0996 -

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Basic information

Entry
Database: PDB / ID: 5mui
TitleGlycoside hydrolase BT_0996
ComponentsBeta-galactosidase
KeywordsHYDROLASE / glycoside hydrolase / arabinofuranosidase / plant pectin / RGII
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Malectin domain / Malectin domain / 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 ...Malectin domain / Malectin domain / 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 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBasle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
iotechnology and Biological Research CouncilBB/K020358/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/K001949/1 United Kingdom
European Research Council322820 United Kingdom
Wellcome TrustWT097907MA United Kingdom
CitationJournal: Nature / Year: 2017
Title: Complex pectin metabolism by gut bacteria reveals novel catalytic functions.
Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / ...Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / Field, R.A. / Zhu, Y. / O'Neill, M.A. / Urbanowicz, B.R. / York, W.S. / Davies, G.J. / Abbott, D.W. / Ralet, M.C. / Martens, E.C. / Henrissat, B. / Gilbert, H.J.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 12, 2017Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type
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 / database_PDB_caveat / 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_chiral / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.1May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8792
Polymers43,6311
Non-polymers1,2471
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint21 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.180, 80.740, 51.410
Angle α, β, γ (deg.)90.00, 114.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-galactosidase


Mass: 43631.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Gene: BT_0996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A921
#2: Polysaccharide beta-L-arabinofuranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-3)]alpha-L- ...beta-L-arabinofuranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-3)]alpha-L-arabinopyranose-(1-4)-[4-O-[(1R)-1-hydroxyethyl]-2-O-methyl-alpha-L-fucopyranose-(1-2)]beta-D-galactopyranose-(1-2)-alpha-D-aceric acid-(1-3)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 1247.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][a-L-Rhap]{[(3+1)][a-D-5-deoxy-Xylf]{[(2+1)][b-D-Galp]{[(2+1)][a-L-Fucp2Me4Ac]{}[(4+1)][a-L-Arap]{[(2+1)][a-L-Rhap]{[(2+1)][b-L-Araf]{}}[(3+1)][a-L-Rhap]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 and 0.2 M Lithium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.77→45.48 Å / Num. obs: 36153 / % possible obs: 99.8 % / Redundancy: 3.7 % / Net I/σ(I): 11.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BT0996

Resolution: 1.77→45.48 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.011 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1703 4.7 %RANDOM
Rwork0.1745 ---
obs0.17597 34428 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å2-0 Å2-0.04 Å2
2---0.73 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.77→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 85 161 3054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193007
X-RAY DIFFRACTIONr_bond_other_d0.0020.022594
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9474088
X-RAY DIFFRACTIONr_angle_other_deg0.99536002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2323.357140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76615438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5431515
X-RAY DIFFRACTIONr_chiral_restr0.1020.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02669
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_it1.5342.3181412
X-RAY DIFFRACTIONr_mcbond_other1.5342.3171411
X-RAY DIFFRACTIONr_mcangle_it2.3053.4671765
X-RAY DIFFRACTIONr_mcangle_other2.3043.4671766
X-RAY DIFFRACTIONr_scbond_it2.2752.6461595
X-RAY DIFFRACTIONr_scbond_other2.2742.6461595
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.573.8612324
X-RAY DIFFRACTIONr_long_range_B_refined4.94626.5213100
X-RAY DIFFRACTIONr_long_range_B_other4.94626.543101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 155 -
Rwork0.288 2500 -
obs--99.74 %

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