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Basic information

Entry
Database: PDB / ID: 6t2s
TitleProminent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown
ComponentsGlycoside hydrolase family 16 protein
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 / Glycoside hydrolase family 16 protein
Function and homology information
Biological speciesBacteroides finegoldii DSM 17565 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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: 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
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 / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glycoside hydrolase family 16 protein
BBB: Glycoside hydrolase family 16 protein
CCC: Glycoside hydrolase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9716
Polymers82,3343
Non-polymers1,6363
Water00
1
AAA: Glycoside hydrolase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9902
Polymers27,4451
Non-polymers5451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glycoside hydrolase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9902
Polymers27,4451
Non-polymers5451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Glycoside hydrolase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9902
Polymers27,4451
Non-polymers5451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.620, 156.620, 197.051
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Glycoside hydrolase family 16 protein


Mass: 27444.811 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides finegoldii DSM 17565 (bacteria)
Gene: DXB57_07550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E5CV05
#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.: 3
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
Has ligand of interestN

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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: 4.24 Å3/Da / Density % sol: 70.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1 M lithuim chloride, 1 M sodium citrate pH 4.0 and 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3.3→197.05 Å / Num. obs: 22156 / % possible obs: 100 % / Redundancy: 21.2 % / CC1/2: 0.992 / Net I/σ(I): 5.1
Reflection shellResolution: 3.3→3.56 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4469 / CC1/2: 0.679

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
GDAdata collection
Aimlessdata scaling
PHASERphasing
Cootmodel building
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→135.637 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.865 / SU B: 52 / SU ML: 0.361 / Cross valid method: FREE R-VALUE / ESU R Free: 0.452
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2533 1097 4.966 %
Rwork0.1991 --
all0.202 --
obs-22092 99.937 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.144 Å2
Baniso -1Baniso -2Baniso -3
1--0.885 Å2-0.443 Å2-0 Å2
2---0.885 Å2-0 Å2
3---2.871 Å2
Refinement stepCycle: LAST / Resolution: 3.3→135.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5811 0 111 0 5922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136099
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175364
X-RAY DIFFRACTIONr_angle_refined_deg2.0261.6658292
X-RAY DIFFRACTIONr_angle_other_deg1.2731.60212459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1515720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0323.091330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.34715942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4231530
X-RAY DIFFRACTIONr_chiral_restr0.0760.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026801
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021356
X-RAY DIFFRACTIONr_nbd_refined0.240.21344
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.25654
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22838
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2152
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0750.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2230.218
X-RAY DIFFRACTIONr_nbd_other0.2240.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.23
X-RAY DIFFRACTIONr_mcbond_it1.6433.4222889
X-RAY DIFFRACTIONr_mcbond_other1.6433.4222888
X-RAY DIFFRACTIONr_mcangle_it2.7945.133606
X-RAY DIFFRACTIONr_mcangle_other2.7945.1313607
X-RAY DIFFRACTIONr_scbond_it1.6663.6473210
X-RAY DIFFRACTIONr_scbond_other1.663.6473210
X-RAY DIFFRACTIONr_scangle_it2.7755.3984686
X-RAY DIFFRACTIONr_scangle_other2.7775.44687
X-RAY DIFFRACTIONr_lrange_it4.79239.0256886
X-RAY DIFFRACTIONr_lrange_other4.79239.0376887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.3-3.3860.33790.29615200.29715990.8270.8251000.287
3.386-3.4780.331720.28514950.28715680.7920.81799.93620.271
3.478-3.5790.381800.27414230.2815040.7780.81699.93350.261
3.579-3.6890.264610.25714050.25714680.8640.87899.86380.238
3.689-3.810.295660.23113750.23414420.8630.8999.93060.212
3.81-3.9440.289790.22913060.23313850.8840.91000.207
3.944-4.0930.192540.19812740.19813300.9440.93399.84960.175
4.093-4.2590.23670.16612290.16912960.9360.9531000.147
4.259-4.4490.181700.14511750.14712450.9580.9631000.127
4.449-4.6660.165520.12311430.12511950.9630.9721000.108
4.666-4.9180.212530.1310860.13311390.9440.971000.113
4.918-5.2150.228370.1410530.14310900.9480.9691000.124
5.215-5.5750.249510.1529630.15710150.9510.96499.90150.136
5.575-6.0210.171510.1619040.1619550.9610.9621000.145
6.021-6.5940.222580.188290.1838870.9530.9531000.16
6.594-7.370.238540.1547570.168110.9520.9621000.14
7.37-8.5060.248410.1686850.1727270.9430.95899.86240.156
8.506-10.4080.297370.1955920.26290.9110.9621000.187
10.408-14.6760.288230.2394770.2415000.9120.9431000.233
14.676-135.6370.453120.4283030.4293200.8810.77698.43751.105
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)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)
14.47730.42550.09022.7698-0.48083.01110.01830.1866-0.1635-0.06860.0894-0.0870.0570.3406-0.10770.05350.0925-0.01970.2046-0.0560.022462.518266.6687134.772
26.1915-3.70810.12215.6505-0.73681.6105-0.1511-0.72010.02720.00530.355-0.00190.1234-0.1733-0.20390.19160.0986-0.06670.26030.01250.110351.991947.8577101.3338
33.5966-0.8224-0.21172.7209-0.42323.3312-0.0072-0.14980.3793-0.00260.1871-0.1679-0.70310.376-0.17990.4713-0.05160.14840.1486-0.1280.2147.04390.146693.3782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA36 - 276
2X-RAY DIFFRACTION2ALLBBB36 - 276
3X-RAY DIFFRACTION3ALLCCC36 - 276

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