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- PDB-8axs: Sialidases and Fucosidases of Akkermansia muciniphila are key for... -

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Basic information

Entry
Database: PDB / ID: 8axs
TitleSialidases and Fucosidases of Akkermansia muciniphila are key for rapid growth on colonic mucin and nutrient sharing amongst mucin-associated human gut microbiota
Components(Exo-alpha-sialidase) x 2
KeywordsHYDROLASE / Sialidase / Neuraminidase
Function / homology
Function and homology information


BNR repeat-like domain / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / IMIDAZOLE / N-acetyl-beta-neuraminic acid / Exo-alpha-sialidase
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSakanaka, H. / Nielsen, T.S. / Pichler, M.J. / Nordberg Karlsson, E. / Abou Hachem, M. / Morth, J.P.
Funding support Denmark, Iraq, 2items
OrganizationGrant numberCountry
Danish Council for Independent Research1026-00386B Denmark
Other governmentIraq
CitationJournal: Nat Commun / Year: 2023
Title: Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria.
Authors: Shuoker, B. / Pichler, M.J. / Jin, C. / Sakanaka, H. / Wu, H. / Gascuena, A.M. / Liu, J. / Nielsen, T.S. / Holgersson, J. / Nordberg Karlsson, E. / Juge, N. / Meier, S. / Morth, J.P. / ...Authors: Shuoker, B. / Pichler, M.J. / Jin, C. / Sakanaka, H. / Wu, H. / Gascuena, A.M. / Liu, J. / Nielsen, T.S. / Holgersson, J. / Nordberg Karlsson, E. / Juge, N. / Meier, S. / Morth, J.P. / Karlsson, N.G. / Abou Hachem, M.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exo-alpha-sialidase
B: Exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,62020
Polymers128,6412
Non-polymers1,97918
Water25,5091416
1
A: Exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,44311
Polymers64,3631
Non-polymers1,08110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exo-alpha-sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1769
Polymers64,2781
Non-polymers8988
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.070, 51.780, 118.440
Angle α, β, γ (deg.)90.000, 93.070, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Exo-alpha-sialidase


Mass: 64362.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: HXS70_08015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G6DVF6
#2: Protein Exo-alpha-sialidase


Mass: 64278.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: HXS70_08015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G6DVF6

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Sugars , 2 types, 4 molecules

#3: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8

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Non-polymers , 6 types, 1430 molecules

#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1416 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 18% PEG 3350,0.1 M BIS TRIS, 0.2 M MgCl2 / PH range: 5 - 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.3→59.135 Å / Num. obs: 308465 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 16.71 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.069 / Rsym value: 0.066 / Net I/σ(I): 12.14
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 4 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 22149 / CC1/2: 0.44 / Rrim(I) all: 1 / Rsym value: 1.7 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold model

Resolution: 1.3→50.25 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1876 14930 5.03 %
Rwork0.1661 563497 -
obs0.1672 296679 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.41 Å2
Refinement stepCycle: LAST / Resolution: 1.3→50.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8999 0 130 1416 10545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01169566
X-RAY DIFFRACTIONf_angle_d1.223812996
X-RAY DIFFRACTIONf_chiral_restr0.09561375
X-RAY DIFFRACTIONf_plane_restr0.01441713
X-RAY DIFFRACTIONf_dihedral_angle_d8.17421313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.46637840.443315396X-RAY DIFFRACTION80.19
1.31-1.330.410910190.414317933X-RAY DIFFRACTION93.09
1.33-1.350.39219310.391618250X-RAY DIFFRACTION94.87
1.35-1.360.37149490.371918558X-RAY DIFFRACTION96.06
1.36-1.380.35379110.35718606X-RAY DIFFRACTION96.7
1.38-1.40.35179930.339818800X-RAY DIFFRACTION97.35
1.4-1.420.33299850.325518811X-RAY DIFFRACTION98.08
1.42-1.440.319710040.314518879X-RAY DIFFRACTION98.31
1.44-1.460.30710730.301718803X-RAY DIFFRACTION98.3
1.46-1.490.306310840.286818849X-RAY DIFFRACTION98.24
1.49-1.510.283510300.267518889X-RAY DIFFRACTION98.29
1.51-1.540.25489130.259418876X-RAY DIFFRACTION98.09
1.54-1.570.243810250.233919157X-RAY DIFFRACTION98.79
1.57-1.60.234410350.206618882X-RAY DIFFRACTION98.78
1.6-1.640.2229660.191619082X-RAY DIFFRACTION98.98
1.64-1.680.2198530.185719173X-RAY DIFFRACTION98.91
1.68-1.720.19619580.170219049X-RAY DIFFRACTION98.94
1.72-1.760.186210970.164318918X-RAY DIFFRACTION98.82
1.76-1.820.175710680.159518915X-RAY DIFFRACTION98.7
1.82-1.870.17179660.154618998X-RAY DIFFRACTION98.8
1.87-1.940.1749840.151419067X-RAY DIFFRACTION98.89
1.94-2.020.180210580.149118991X-RAY DIFFRACTION98.85
2.02-2.110.162210990.140218868X-RAY DIFFRACTION98.69
2.11-2.220.167510410.135919061X-RAY DIFFRACTION99.25
2.22-2.360.16759400.132719229X-RAY DIFFRACTION99.33
2.36-2.540.153610940.130618947X-RAY DIFFRACTION99.34
2.54-2.80.16129360.137819211X-RAY DIFFRACTION99.51
2.8-3.210.163610500.141319080X-RAY DIFFRACTION99.14
3.21-4.040.162310760.138119077X-RAY DIFFRACTION99.45
4.04-50.250.15259390.137519142X-RAY DIFFRACTION99.26

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