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Basic information

Entry
Database: PDB / ID: 6t2o
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: 2.05 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 1.1Aug 26, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.2Jan 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)64,8298
Polymers64,5002
Non-polymers3286
Water2,414134
1
AAA: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4144
Polymers32,2501
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glycosyl hydrolase family 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4144
Polymers32,2501
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.646, 82.646, 121.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Glycosyl hydrolase family 16


Mass: 32250.236 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium malonate pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.05→82.65 Å / Num. obs: 51105 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.986 / Net I/σ(I): 6.3
Reflection shellResolution: 2.05→2.16 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3974 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
DIALSdata reduction
PHASERphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILN

3iln


Resolution: 2.05→82.646 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.687 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2402 2613 5.12 %
Rwork0.1994 --
all0.202 --
obs-51036 99.941 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.382 Å20 Å20 Å2
2---0.382 Å20 Å2
3---0.765 Å2
Refinement stepCycle: LAST / Resolution: 2.05→82.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 18 134 4071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134045
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173626
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.6425480
X-RAY DIFFRACTIONr_angle_other_deg1.2581.588431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.585481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3723.756221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17715668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0391516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
X-RAY DIFFRACTIONr_nbd_refined0.1880.2662
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.23349
X-RAY DIFFRACTIONr_nbtor_refined0.170.21871
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21945
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2171
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2650.213
X-RAY DIFFRACTIONr_nbd_other0.1890.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5910.26
X-RAY DIFFRACTIONr_mcbond_it1.2042.8321930
X-RAY DIFFRACTIONr_mcbond_other1.2042.8321929
X-RAY DIFFRACTIONr_mcangle_it1.7794.2412409
X-RAY DIFFRACTIONr_mcangle_other1.7784.2422410
X-RAY DIFFRACTIONr_scbond_it1.58732115
X-RAY DIFFRACTIONr_scbond_other1.58632116
X-RAY DIFFRACTIONr_scangle_it2.4544.4223071
X-RAY DIFFRACTIONr_scangle_other2.4544.4223072
X-RAY DIFFRACTIONr_lrange_it4.19131.6334421
X-RAY DIFFRACTIONr_lrange_other4.17531.5374407
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
2.05-2.1030.3021870.29335930.29437870.8130.78899.81520.287
2.103-2.1610.2771800.25434800.25536620.8560.86899.94540.246
2.161-2.2240.2671700.24133630.24235350.8790.88799.94340.228
2.224-2.2920.2761990.2732780.2734920.8830.87899.57040.257
2.292-2.3670.2841700.21931920.22233620.8980.9171000.206
2.367-2.450.2831710.21630640.21932360.8980.92399.96910.203
2.45-2.5420.2941380.22129990.22431380.8870.9299.96810.209
2.542-2.6460.2811780.21528410.21930190.9040.9251000.207
2.646-2.7640.2311530.21427650.21529190.9160.92299.96570.208
2.764-2.8980.2541560.21325950.21627510.9240.9311000.212
2.898-3.0550.251360.21825060.21926420.9090.9211000.222
3.055-3.240.2871270.2223610.22324880.8910.921000.228
3.24-3.4630.2251110.21122480.21223590.9410.941000.224
3.463-3.740.221060.20520850.20621910.9480.9511000.222
3.74-4.0960.2091060.1819010.18220070.9520.961000.203
4.096-4.5790.197950.14117340.14418290.9610.971000.172
4.579-5.2840.198690.14515410.14716100.9620.9761000.173
5.284-6.4650.228610.17513070.17713680.9620.9661000.203
6.465-9.1150.194660.1710000.17110660.9560.9641000.193
9.115-82.6460.299340.2295690.2346040.9630.95599.83440.254
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)
11.38430.59870.0813.43380.54682.0476-0.02970.09840.0455-0.0104-0.04840.1366-0.0705-0.19370.07820.08320.03990.02010.04280.00470.014-35.038-21.15330.3163
23.1189-0.0410.34921.4163-0.08912.5605-0.0036-0.22240.02030.0167-0.0051-0.0812-0.12230.10550.00860.016-0.0052-0.02290.0823-0.01070.0536-17.0618-22.067630.9439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA34 - 274
2X-RAY DIFFRACTION2ALLBBB33 - 401

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