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

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Basic information

Entry
Database: PDB / ID: 8ayr
TitleSialidases and Fucosidases of Akkermansia muciniphila are key for rapid growth on colonic mucin and nutrient sharing amongst mucin-associated human gut microbiota
ComponentsCoagulation factor 5/8 type domain protein
KeywordsHYDROLASE / Sialidase / Neuraminidase
Function / homology
Function and homology information


alpha-L-fucosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Chitobiase/beta-hexosaminidase C-terminal domain / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily ...Chitobiase/beta-hexosaminidase C-terminal domain / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Coagulation factor 5/8 type domain protein
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionSep 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 2.0Mar 15, 2023Group: Advisory / Atomic model / Category: atom_site / pdbx_unobs_or_zero_occ_residues / Item: _atom_site.occupancy
Revision 2.1Apr 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 2.2Apr 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.3May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor 5/8 type domain protein
B: Coagulation factor 5/8 type domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5546
Polymers155,3942
Non-polymers1604
Water36020
1
A: Coagulation factor 5/8 type domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7773
Polymers77,6971
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coagulation factor 5/8 type domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7773
Polymers77,6971
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.190, 76.450, 84.500
Angle α, β, γ (deg.)88.410, 89.080, 88.230
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 30 through 128 or resid 130...
d_2ens_1(chain "B" and (resid 30 through 128 or resid 130...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1CYSGLYA2 - 100
d_12ens_1GLYSERA102 - 109
d_13ens_1ALAGLYA111 - 220
d_14ens_1ALALEUA222 - 235
d_15ens_1ALASERA237 - 449
d_16ens_1ALAVALA451 - 465
d_17ens_1LEUALAA467 - 485
d_18ens_1VALTYRA488 - 506
d_19ens_1ASNTRPA508 - 543
d_110ens_1VALALAA545 - 627
d_111ens_1GLYILEA629 - 634
d_112ens_1ALALYSA636 - 659
d_113ens_1VALLYSA661 - 677
d_21ens_1CYSGLYB1 - 99
d_22ens_1GLYSERB101 - 108
d_23ens_1ALAGLYB110 - 219
d_24ens_1ALALEUB221 - 234
d_25ens_1ALASERB236 - 448
d_26ens_1ALAVALB450 - 464
d_27ens_1LEUALAB466 - 484
d_28ens_1VALTYRB487 - 505
d_29ens_1ASNTRPB507 - 542
d_210ens_1VALALAB544 - 626
d_211ens_1GLYILEB628 - 633
d_212ens_1ALALYSB635 - 658
d_213ens_1VALLYSB660 - 676

NCS oper: (Code: givenMatrix: (-0.994644931747, -0.0699476186579, 0.0760841007926), (-0.0744662726535, -0.0254566162435, -0.996898557992), (0.0716675239311, -0.997225797567, 0.0201115558835)Vector: ...NCS oper: (Code: given
Matrix: (-0.994644931747, -0.0699476186579, 0.0760841007926), (-0.0744662726535, -0.0254566162435, -0.996898557992), (0.0716675239311, -0.997225797567, 0.0201115558835)
Vector: 10.6800079712, 38.0084737161, 30.6521295221)

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Components

#1: Protein Coagulation factor 5/8 type domain protein


Mass: 77696.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: Amuc_0846 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UQE4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.7 / Details: 0.1 M Hepes, 16% PEG10k, / PH range: 7.2 -7.8

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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: 0.9763 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→34.51 Å / Num. obs: 99265 / % possible obs: 90.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 59.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08178 / Rpim(I) all: 0.04795 / Rrim(I) all: 0.09486 / Net I/σ(I): 9.93
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.745 / Num. unique obs: 2720 / CC1/2: 0.843 / Rrim(I) all: 0.812 / % possible all: 71

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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

Resolution: 2.7→34.51 Å / SU ML: 0.4434 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 38.0663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2754 2450 5.19 %
Rwork0.2331 44730 -
obs0.2353 47180 90.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.87 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10602 0 4 20 10626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004610902
X-RAY DIFFRACTIONf_angle_d0.861914843
X-RAY DIFFRACTIONf_chiral_restr0.05081556
X-RAY DIFFRACTIONf_plane_restr0.00751943
X-RAY DIFFRACTIONf_dihedral_angle_d5.74411511
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.61691827221 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.44891090.44581901X-RAY DIFFRACTION68.55
2.75-2.810.45721220.39232362X-RAY DIFFRACTION85.01
2.81-2.870.45571110.3612508X-RAY DIFFRACTION91.16
2.87-2.940.3771560.3442536X-RAY DIFFRACTION92
2.94-3.010.43851520.33452461X-RAY DIFFRACTION91.24
3.01-3.090.40831450.32992483X-RAY DIFFRACTION91.22
3.09-3.180.40251530.33112540X-RAY DIFFRACTION91.66
3.18-3.290.3561760.30112444X-RAY DIFFRACTION91
3.29-3.40.35331710.2762471X-RAY DIFFRACTION90.76
3.4-3.540.31871440.26842521X-RAY DIFFRACTION92.06
3.54-3.70.27321000.24732612X-RAY DIFFRACTION93.87
3.7-3.90.28241290.22922544X-RAY DIFFRACTION92.36
3.9-4.140.23551150.20952563X-RAY DIFFRACTION92.5
4.14-4.460.22541420.19632525X-RAY DIFFRACTION91.68
4.46-4.910.20751440.17162482X-RAY DIFFRACTION90.96
4.91-5.610.21571430.18932595X-RAY DIFFRACTION93.99
5.61-7.060.19961010.20492631X-RAY DIFFRACTION93.98
7.06-34.510.19981370.17132551X-RAY DIFFRACTION92.79
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)
11.105067062860.779076858570.7732010394231.144091750741.249314711362.84255776843-0.181064989876-0.06713630913890.149804084092-0.115724173361-0.1955490636860.215245453447-0.222649773184-0.507840649818-0.0001404745108840.734149857930.1161040951290.003294721858010.69381946887-0.02119329523560.772672303299-12.058291592934.9904584973-40.6449129974
20.2064725960390.139211393686-0.1742663144580.197528551367-0.2046780928580.218929955261-0.2947311336050.295624857378-0.57394977626-0.391686930340.350051256262-0.2540543049480.185461779291-0.3200976250540.000193133999160.914624399354-0.1348366224190.1694144998621.02888161084-0.2768855229361.31824942995-26.06182186990.559773127634-39.6352762289
30.8801220876430.7936895908550.2948428309771.083761995990.7802551582230.8121788379170.429068581764-0.740822807493-0.1899360931070.381473974311-0.44970674289-0.362710110325-0.4509176069430.2946927707770.0004218566731860.895293158677-0.1384056520890.006452165104170.8643504514470.05615368947671.27039387967-37.2078403524-6.15328819469-14.406314052
41.00514432834-0.152359400408-0.07318647478431.958969816290.911183006391.257719507080.044846786983-0.1581408311580.001960879134910.04497551090530.0497946814076-0.1729312199410.0285651596780.0312508746822-1.26946685151E-50.717220571031-0.07921757954557.8267542835E-50.7467551844230.08619302414340.5909728796330.546682759518-3.302149694122.18737959778
50.157375792590.040051191468-0.1773821224310.125631837233-0.06151035621370.2011976810820.3318893344770.6184130713390.0950021132385-0.5122245878650.017103761461-0.04744260821360.07587787915410.2100384245350.0006180126736771.13467010475-0.09675022815480.2788690559321.1793025830.02706044709010.98005603784912.7076209128-1.58378013435-33.8934489604
60.3223676206820.379053500547-0.1353620282190.492026517605-0.0531660610330.2643819980970.120125280222-0.05486021362290.6717825609810.07928202957190.412302582876-0.134538170892-0.2452478412050.09521872974020.0003779364688311.301692117870.03078041619710.3443779832311.66579351969-0.08960700009841.3859577892225.456926463921.1339850095-41.6601611636
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 484 )AA29 - 4841 - 456
22chain 'A' and (resid 485 through 536 )AA485 - 536457 - 508
33chain 'A' and (resid 537 through 705 )AA537 - 705509 - 677
44chain 'B' and (resid 30 through 484 )BB30 - 4841 - 455
55chain 'B' and (resid 485 through 536 )BB485 - 536456 - 507
66chain 'B' and (resid 537 through 705 )BB537 - 705508 - 676

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