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

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Basic information

Entry
Database: PDB / ID: 8axt
TitleSialidases and Fucosidases of Akkermansia muciniphila are key for rapid growth on colonic mucin and nutrient sharing amongst mucin-associated human gut microbiota
ComponentsSialidase domain-containing protein
KeywordsHYDROLASE / Sialidase / Neuraminidase
Function / homologyBNR repeat-like domain / Sialidase / Sialidase superfamily / metal ion binding / Sialidase domain-containing protein
Function and homology information
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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: Sialidase domain-containing protein
B: Sialidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5569
Polymers130,2992
Non-polymers2577
Water23,9241328
1
A: Sialidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2253
Polymers65,1491
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialidase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3316
Polymers65,1491
Non-polymers1825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.960, 56.790, 146.720
Angle α, β, γ (deg.)90.000, 94.550, 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

#1: Protein Sialidase domain-containing protein


Mass: 65149.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: Amuc_1547 / Production host: Escherichia coli (E. coli) / References: UniProt: B2ULI1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1328 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 25% PEG 3350, 0.1 M Bis tris, 0.2 MgCl2 / PH range: 5 -6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.59→146.258 Å / Num. obs: 160846 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.12 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.3 / Rrim(I) all: 0.32 / Net I/σ(I): 6.7
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1 / Num. unique obs: 11798 / CC1/2: 0.32 / R split: 1 / Rpim(I) all: 1 / Rrim(I) all: 1 / Rsym value: 1 / % possible all: 99.8

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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: alpha fold model

Resolution: 1.59→72.73 Å / SU ML: 0.1928 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.202 8029 4.99 %
Rwork0.1683 152764 -
obs0.17 160793 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.75 Å2
Refinement stepCycle: LAST / Resolution: 1.59→72.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8994 0 7 1328 10329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00959248
X-RAY DIFFRACTIONf_angle_d1.051312540
X-RAY DIFFRACTIONf_chiral_restr0.0611322
X-RAY DIFFRACTIONf_plane_restr0.01211648
X-RAY DIFFRACTIONf_dihedral_angle_d6.84331247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.30962520.30084991X-RAY DIFFRACTION99.83
1.61-1.630.33782740.29455137X-RAY DIFFRACTION99.71
1.63-1.650.33732790.28724993X-RAY DIFFRACTION99.57
1.65-1.670.29812830.2765104X-RAY DIFFRACTION99.78
1.67-1.690.30142700.24585009X-RAY DIFFRACTION99.87
1.69-1.710.27762530.23765112X-RAY DIFFRACTION99.8
1.71-1.740.29012340.23595108X-RAY DIFFRACTION99.83
1.74-1.760.2832660.23535015X-RAY DIFFRACTION99.91
1.76-1.790.25952710.22655067X-RAY DIFFRACTION99.78
1.79-1.820.26342630.21135109X-RAY DIFFRACTION99.74
1.82-1.850.24072690.19925065X-RAY DIFFRACTION99.93
1.85-1.890.21272650.1925063X-RAY DIFFRACTION99.87
1.89-1.920.21492930.18765058X-RAY DIFFRACTION99.76
1.92-1.960.22972630.17775095X-RAY DIFFRACTION99.94
1.96-20.19742610.15865044X-RAY DIFFRACTION99.72
2-2.050.20292580.15725089X-RAY DIFFRACTION99.87
2.05-2.10.19642910.15995118X-RAY DIFFRACTION99.96
2.1-2.160.19622620.1575065X-RAY DIFFRACTION99.78
2.16-2.220.20022750.15645058X-RAY DIFFRACTION99.79
2.22-2.290.19992660.16215094X-RAY DIFFRACTION99.76
2.29-2.380.19282840.14455122X-RAY DIFFRACTION99.94
2.38-2.470.16512220.13765120X-RAY DIFFRACTION99.96
2.47-2.580.1832950.14365105X-RAY DIFFRACTION99.91
2.58-2.720.1852580.14775117X-RAY DIFFRACTION99.87
2.72-2.890.19472630.15175084X-RAY DIFFRACTION99.79
2.89-3.110.18222780.165094X-RAY DIFFRACTION99.81
3.11-3.430.17822850.15385157X-RAY DIFFRACTION99.63
3.43-3.920.16852590.1475105X-RAY DIFFRACTION99.41
3.92-4.940.15852680.1315178X-RAY DIFFRACTION99.56
4.94-72.730.1962690.17195288X-RAY DIFFRACTION99.06
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.39663248796-0.277020410669-0.5778566591990.693945634076-0.1788318613141.138580193090.04864293542090.1031065026380.120252416262-0.03071930576950.03509051513540.0349524963476-0.119501477128-0.182033373841-0.09044954791530.119606459510.0183124500066-0.004530955861580.1370707800010.02731820471520.139425787488.7128201575716.08461439277.95921477592
22.3275132145-0.6057095332580.162276121733.61033998867-0.1868345913231.45143847401-0.031464380343-0.06937305389350.1665451766880.02516092656280.07776734200610.154193715633-0.205112227289-0.238939048257-0.05053634406650.1054722767650.02460418794180.01245574854630.1980560670640.02008332763150.144807296706-3.3950838502912.795639178519.9671806749
30.513036785453-0.0291270207356-0.004008566021180.301319370377-0.02874894651340.480602912872-0.00324963082996-0.0223648745492-0.00338535823535-0.009822779863260.01289976470630.0375370285248-0.0091448130669-0.072675542269-0.01922207415880.0919991711939-0.006545833471-0.004928126538580.0820539175934-0.004179716760180.099736210923721.17404594610.040483127314719.0898378866
40.433679748902-0.0957843325838-0.2045736640950.5127739739590.2086876719381.03739862258-0.0306165434464-0.0962425373814-0.05981968530470.04870432524660.0478524285444-0.06068391803120.1106916086760.121584164424-0.03136510757760.08741943986020.0121715365549-0.003197668308110.09143593430330.008624430116960.11315583976640.5447688245-13.348233447421.9705627166
52.258486953890.2532907082770.5171006133650.7434508908-0.3156654332771.04155723820.039249582258-0.13376595656-0.1442734657590.03407909614660.09770599963110.09268118027520.176911118694-0.305332737449-0.01686154807370.15682801767-0.056236228149-0.01879044567950.1945731516990.05353730729620.1681618920054.5864709515710.976807254461.0616022942
60.9031516425190.570989001945-0.1311988443211.63144053562-0.3605782326980.6443759426460.0407463210790.0785870572761-0.329894336306-0.1797734416040.1630531698370.1817308679980.309297545692-0.4352194428660.1549038980790.180809183552-0.0946293157841-0.06351142481520.336704864140.07989834933680.27139569776-5.7549178056514.432862208247.469538823
71.993804197250.280330845957-0.3687921461480.511463430182-0.2510987883530.7800164371530.01721191780090.09902245249880.0708258130484-0.02491441910280.08692319641060.126218002171-0.0137916442306-0.245533484417-0.03344415977430.1082143623480.00348330932827-0.00275782202790.1743581416140.044781382640.1447846269615.8801104644930.182354488543.4670275302
81.09587456924-0.182758521587-0.1061324056870.57691237356-0.06138111759150.8674256853480.02417024281210.03353392801930.00360237903817-0.03471781816570.04899028892650.0661361037171-0.0365269370543-0.115130870892-0.06587207427660.08057538671060.003243290438650.01785906835430.07316931644680.01097697885940.095864838521616.761184130729.928086821751.1811226278
90.7518719780580.119286725236-0.3615724733320.60709012699-0.06513085778590.7785220104250.0165063267888-0.0195584598972-0.05442655184610.06237600680910.01287184683710.01775799248610.0382681579106-0.00810684152936-0.02201949645330.1209502665910.0158896073172-0.004402895876970.08057379285160.008987784940570.096061845373628.452499430723.080880212658.0678435781
100.7174057672120.1842055569120.1659567250350.801519299160.2351124612271.373802709560.001675580689030.06353201510750.0200630294892-0.01190559067790.0525974298117-0.101607301666-0.06545093806010.279928236944-0.08130957074670.0952729592046-0.01435400273070.001163045627810.108533251020.01273677894270.089080536740340.130469159934.343997802249.6559408182
111.44222349304-0.1502241958770.3359771419571.066883215040.01808042279851.04893009963-0.03387677178090.1046460103490.1137850029310.04956722637110.00779084691215-0.0649673994988-0.1906275771640.146093759402-0.004447807415150.148897553506-0.03164159656190.006230863517870.09828240964570.01168035552630.1035119304837.202550043243.928875146653.2538804009
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 127 )AA25 - 1271 - 103
22chain 'A' and (resid 128 through 182 )AA128 - 182104 - 158
33chain 'A' and (resid 183 through 436 )AA183 - 436159 - 412
44chain 'A' and (resid 437 through 595 )AA437 - 595413 - 571
55chain 'B' and (resid 25 through 127 )BB25 - 1271 - 103
66chain 'B' and (resid 128 through 182 )BB128 - 182104 - 158
77chain 'B' and (resid 183 through 250 )BB183 - 250159 - 226
88chain 'B' and (resid 251 through 333 )BB251 - 333227 - 309
99chain 'B' and (resid 334 through 436 )BB334 - 436310 - 412
1010chain 'B' and (resid 437 through 492 )BB437 - 492413 - 468
1111chain 'B' and (resid 493 through 595 )BB493 - 595469 - 571

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