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- PDB-6t2n: Prominent members of the human gut microbiota express endo-acting... -

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Basic information

Entry
Database: PDB / ID: 6t2n
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 speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
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: Glycoside hydrolase family 16 protein
BBB: Glycoside hydrolase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4624
Polymers73,3822
Non-polymers802
Water00
1
AAA: Glycoside hydrolase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7312
Polymers36,6911
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Glycoside hydrolase family 16 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7312
Polymers36,6911
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.465, 96.128, 128.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycoside hydrolase family 16 protein


Mass: 36690.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: C1I88_04035, CXT92_05930, EYB66_02710 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N8IRP0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Tri sodium citrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.7→19.9 Å / Num. obs: 33933 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.991 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.83 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4096 / CC1/2: 0.485

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
Cootmodel building
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WUT

5wut


Resolution: 2.7→19.716 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: FREE R-VALUE / ESU R: 0.409 / ESU R Free: 0.304
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2811 1464 4.82 %
Rwork0.2334 --
all0.236 --
obs-30371 99.574 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.638 Å2
Baniso -1Baniso -2Baniso -3
1-3.102 Å20 Å2-0 Å2
2---4.325 Å20 Å2
3---1.223 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 2 0 4472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134598
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174184
X-RAY DIFFRACTIONr_angle_refined_deg2.2021.6516234
X-RAY DIFFRACTIONr_angle_other_deg2.4561.5849750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1415554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40422.991234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63915782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7831522
X-RAY DIFFRACTIONr_chiral_restr0.0880.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025104
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02986
X-RAY DIFFRACTIONr_nbd_refined0.230.2922
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2370.24015
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22087
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1040.22073
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2890.210
X-RAY DIFFRACTIONr_nbd_other0.2860.231
X-RAY DIFFRACTIONr_mcbond_it3.0727.3092222
X-RAY DIFFRACTIONr_mcbond_other3.0727.3072221
X-RAY DIFFRACTIONr_mcangle_it4.85710.9652774
X-RAY DIFFRACTIONr_mcangle_other4.85710.9662775
X-RAY DIFFRACTIONr_scbond_it3.3057.5932376
X-RAY DIFFRACTIONr_scbond_other3.3047.5942377
X-RAY DIFFRACTIONr_scangle_it5.36611.2413460
X-RAY DIFFRACTIONr_scangle_other5.36511.2423461
X-RAY DIFFRACTIONr_lrange_it7.69481.7355031
X-RAY DIFFRACTIONr_lrange_other7.69381.6955029
LS refinement shellResolution: 11.936→19.716 Å
RfactorNum. reflection% reflection
Rfree0.351 10 -
Rwork0.257 304 -
obs--75.6627 %

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