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- PDB-6t2r: Prominent members of the human gut microbiota express endo-acting... -

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Basic information

Entry
Database: PDB / ID: 6t2r
TitleProminent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown
ComponentsBeta-glycosidase
KeywordsHYDROLASE / Human gut microbiota / mucin degradation / O-glycanases / GH16 / endo beta-galactosidase
Function / homology
Function and homology information


licheninase / licheninase activity / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Category: citation / citation_author
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6813
Polymers30,4891
Non-polymers1922
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-32 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.928, 87.135, 156.193
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Beta-glycosidase / Glycoside hydrolase family 16 protein


Mass: 30488.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria)
Gene: bglA_5, DW190_07485, DW794_15185, DWY26_17235, DWZ35_07795, DXA49_02580, EAJ00_16275, ERS852494_03890
Production host: Escherichia coli (E. coli) / References: UniProt: A0A174TK78, licheninase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1 M ammonium sulfate

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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: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→43.57 Å / Num. obs: 19202 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.995 / Net I/σ(I): 1.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1554 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
DIALSdata reduction
PHASERphasing
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ILN

3iln


Resolution: 2.1→43.57 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.295 / SU ML: 0.155 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.242 950 4.961 %
Rwork0.1972 --
all0.199 --
obs-19149 99.901 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.623 Å2
Baniso -1Baniso -2Baniso -3
1--1.867 Å2-0 Å2-0 Å2
2--4.613 Å20 Å2
3----2.745 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 10 126 2171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132112
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171811
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6442884
X-RAY DIFFRACTIONr_angle_other_deg1.3121.5774207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7635247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79222.54126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43215321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2311513
X-RAY DIFFRACTIONr_chiral_restr0.0710.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022394
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
X-RAY DIFFRACTIONr_nbd_refined0.2010.2368
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21771
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2980
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2125
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.225
X-RAY DIFFRACTIONr_nbd_other0.2630.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3050.210
X-RAY DIFFRACTIONr_mcbond_it2.7583.287991
X-RAY DIFFRACTIONr_mcbond_other2.7573.286990
X-RAY DIFFRACTIONr_mcangle_it3.9794.921237
X-RAY DIFFRACTIONr_mcangle_other3.9784.921238
X-RAY DIFFRACTIONr_scbond_it3.513.4731121
X-RAY DIFFRACTIONr_scbond_other3.473.4611113
X-RAY DIFFRACTIONr_scangle_it4.8885.1061647
X-RAY DIFFRACTIONr_scangle_other4.8155.0871635
X-RAY DIFFRACTIONr_lrange_it6.30736.832372
X-RAY DIFFRACTIONr_lrange_other6.28136.6662354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.276760.2891332X-RAY DIFFRACTION99.5757
2.155-2.2140.285830.2471244X-RAY DIFFRACTION99.7744
2.214-2.2780.306680.251259X-RAY DIFFRACTION100
2.278-2.3480.309550.2361251X-RAY DIFFRACTION99.9235
2.348-2.4250.288460.2291169X-RAY DIFFRACTION99.8357
2.425-2.510.302650.2181154X-RAY DIFFRACTION99.7545
2.51-2.6040.271550.2141137X-RAY DIFFRACTION99.9162
2.604-2.710.289680.2051032X-RAY DIFFRACTION100
2.71-2.8310.299570.1941011X-RAY DIFFRACTION100
2.831-2.9690.274460.202998X-RAY DIFFRACTION100
2.969-3.1290.231440.198965X-RAY DIFFRACTION100
3.129-3.3190.283520.212885X-RAY DIFFRACTION100
3.319-3.5470.228210.2856X-RAY DIFFRACTION100
3.547-3.8310.245330.181783X-RAY DIFFRACTION100
3.831-4.1960.188450.164726X-RAY DIFFRACTION100
4.196-4.6890.148300.134667X-RAY DIFFRACTION99.8567
4.689-5.4110.22280.153590X-RAY DIFFRACTION100
5.411-6.6190.208360.196493X-RAY DIFFRACTION99.8113
6.619-9.3280.173280.188402X-RAY DIFFRACTION100
9.328-43.570.199140.209245X-RAY DIFFRACTION100

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