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Basic information

Entry
Database: PDB / ID: 6t2q
TitleProminent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown
ComponentsGlycosyl hydrolase family 16
KeywordsHYDROLASE / Human gut microbiota / mucin degradation / O-glycanases / GH16 / endo beta-galactosidase
Function / homologyGlycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Glycosyl hydrolase family 16
Function and homology information
Biological speciesBacteroides caccae ATCC 43185 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCrouch, L.I. / Liberato, M.V. / Ubranowicz, P.A. / Basle, A. / Lamb, C.A. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. ...Crouch, L.I. / Liberato, M.V. / Ubranowicz, P.A. / Basle, A. / Lamb, C.A. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madubic, K. / Chater, P. / Zhang, F. / Linhardt, R.J. / Spence, D.I.R. / Bolam, D.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M029018/1 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown.
Authors: Crouch, L.I. / Liberato, M.V. / Urbanowicz, P.A. / Basle, A. / Lamb, C.A. / Stewart, C.J. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madunic, K. / Wuhrer, M. / ...Authors: Crouch, L.I. / Liberato, M.V. / Urbanowicz, P.A. / Basle, A. / Lamb, C.A. / Stewart, C.J. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madunic, K. / Wuhrer, M. / Chater, P. / Pearson, J.P. / Glowacki, R. / Martens, E.C. / Zhang, F. / Linhardt, R.J. / Spencer, D.I.R. / Bolam, D.N.
History
DepositionOct 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type
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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.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.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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 26, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Glycosyl hydrolase family 16
BBB: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,93214
Polymers64,4992
Non-polymers1,43312
Water1,78399
1
AAA: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9436
Polymers32,2491
Non-polymers6945
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9898
Polymers32,2491
Non-polymers7407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.918, 82.918, 121.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein / Sugars , 2 types, 4 molecules AAABBB

#1: Protein Glycosyl hydrolase family 16


Mass: 32249.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae ATCC 43185 (bacteria)
Gene: BACCAC_02680 / Production host: Escherichia coli (E. coli) / References: UniProt: A5ZIF0
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 109 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 450 mM sodium malonate pH 7.0, 24 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→19.99 Å / Num. obs: 55261 / % possible obs: 99.2 % / Redundancy: 7.6 % / CC1/2: 0.999 / Net I/σ(I): 14
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4092 / CC1/2: 0.472

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILN

3iln


Resolution: 2→19.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 8.042 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2108 2638 4.777 %
Rwork0.1867 --
all0.188 --
obs-55218 99.873 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.976 Å2
Baniso -1Baniso -2Baniso -3
1--0.615 Å20 Å20 Å2
2---0.615 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 90 99 4108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134124
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173677
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.6665589
X-RAY DIFFRACTIONr_angle_other_deg1.291.6038561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5475483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43823.784222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07815670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2961516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02886
X-RAY DIFFRACTIONr_nbd_refined0.2220.2739
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23432
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21917
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2132
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.215
X-RAY DIFFRACTIONr_nbd_other0.1810.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.570.26
X-RAY DIFFRACTIONr_mcbond_it1.4482.9391932
X-RAY DIFFRACTIONr_mcbond_other1.4482.9371931
X-RAY DIFFRACTIONr_mcangle_it2.1694.3972412
X-RAY DIFFRACTIONr_mcangle_other2.1684.3992413
X-RAY DIFFRACTIONr_scbond_it1.8983.1862192
X-RAY DIFFRACTIONr_scbond_other1.8983.1872193
X-RAY DIFFRACTIONr_scangle_it2.9374.6833176
X-RAY DIFFRACTIONr_scangle_other2.9374.6843177
X-RAY DIFFRACTIONr_lrange_it5.21733.734503
X-RAY DIFFRACTIONr_lrange_other5.21333.6884497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2742170.2973872X-RAY DIFFRACTION99.9267
2.052-2.1080.3351910.2793781X-RAY DIFFRACTION100
2.108-2.1690.2852010.2543672X-RAY DIFFRACTION100
2.169-2.2360.2541630.2313591X-RAY DIFFRACTION100
2.236-2.3090.242080.2143433X-RAY DIFFRACTION99.9725
2.309-2.390.2161850.1973313X-RAY DIFFRACTION100
2.39-2.480.2421410.2043238X-RAY DIFFRACTION100
2.48-2.5810.2571630.2083148X-RAY DIFFRACTION100
2.581-2.6960.2531290.22969X-RAY DIFFRACTION99.9677
2.696-2.8280.2221540.2062855X-RAY DIFFRACTION100
2.828-2.980.2461430.2082713X-RAY DIFFRACTION100
2.98-3.1610.2041080.2052600X-RAY DIFFRACTION99.9631
3.161-3.3790.221030.1992421X-RAY DIFFRACTION100
3.379-3.6490.213840.1912296X-RAY DIFFRACTION100
3.649-3.9970.2041050.1752068X-RAY DIFFRACTION99.9081
3.997-4.4670.1621030.1371872X-RAY DIFFRACTION100
4.467-5.1550.147910.1321668X-RAY DIFFRACTION99.9432
5.155-6.3080.208700.1681401X-RAY DIFFRACTION100
6.308-8.8950.18490.1711105X-RAY DIFFRACTION100
Refinement TLS params.

S11: -0.0288 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6834-0.11790.28333.1773-0.33012.43030.01550.1043-0.21610.0007-0.0167-0.14060.06690.02810.1077-0.01270.01850.00870.02410.11419.265124.5188-15.0329
23.26320.6145-0.60621.3629-0.2282.0769-0.0502-0.10570.0673-0.0322-0.07930.21560.12290.0610.03510.0321-0.01170.0884-0.00980.077220.19156.340415.3602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA33 - 274
2X-RAY DIFFRACTION2ALLBBB34 - 324

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