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- PDB-8pxu: Targeting extended blood antigens by Akkermansia muciniphila enzy... -

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Basic information

Entry
Database: PDB / ID: 8pxu
TitleTargeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / Beta-hexosaminidase / Akkermansia muciniphila / GalNAc-B converting / CBM
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / lysosome / membrane
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
CACODYLATE ION / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsJensen, M. / Abou Hachem, M. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Independent Research Fund Denmark - Technology and Production Sciences0136-00086A Denmark
Citation
Journal: Nat Microbiol / Year: 2024
Title: Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood.
Authors: Jensen, M. / Stenfelt, L. / Ricci Hagman, J. / Pichler, M.J. / Weikum, J. / Nielsen, T.S. / Hult, A. / Morth, J.P. / Olsson, M.L. / Abou Hachem, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year
Revision 1.2May 15, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
B: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,4757
Polymers219,9273
Non-polymers5484
Water13,763764
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4462
Polymers73,3091
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5833
Polymers73,3091
Non-polymers2742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4462
Polymers73,3091
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.707, 170.738, 172.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-N-acetylhexosaminidase


Mass: 73309.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Mutation to the catalytic acid E339A (321 in the sequence provided)
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: Amuc_0369 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UN02
#2: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 11% PEG8000, 0.5 M NaCl, 0.1M NaCacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.99→49.4 Å / Num. obs: 194025 / % possible obs: 99.3 % / Redundancy: 14 % / Biso Wilson estimate: 46.33 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.041 / Rrim(I) all: 0.153 / Net I/σ(I): 9.65
Reflection shellResolution: 1.99→2.061 Å / Mean I/σ(I) obs: 0.56 / Num. unique obs: 268863 / CC1/2: 0.428 / Rpim(I) all: 0.841

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→49.4 Å / SU ML: 0.2994 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 9716 5.01 %
Rwork0.1885 184309 -
obs0.19 194025 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.23 Å2
Refinement stepCycle: LAST / Resolution: 1.99→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15145 0 20 764 15929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006615561
X-RAY DIFFRACTIONf_angle_d0.771521072
X-RAY DIFFRACTIONf_chiral_restr0.05172256
X-RAY DIFFRACTIONf_plane_restr0.00762726
X-RAY DIFFRACTIONf_dihedral_angle_d13.49775733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.38383120.38475978X-RAY DIFFRACTION96.81
2.01-2.040.37343630.36425967X-RAY DIFFRACTION98.72
2.04-2.060.3512990.33446104X-RAY DIFFRACTION98.8
2.06-2.090.33653330.31136019X-RAY DIFFRACTION98.79
2.09-2.110.332870.29216100X-RAY DIFFRACTION98.95
2.11-2.140.27843330.26956064X-RAY DIFFRACTION98.87
2.14-2.170.2772970.25146077X-RAY DIFFRACTION98.96
2.17-2.210.28883620.24326050X-RAY DIFFRACTION98.92
2.21-2.240.27583600.23736047X-RAY DIFFRACTION99.01
2.24-2.280.27073100.23446076X-RAY DIFFRACTION98.96
2.28-2.320.2692980.23826104X-RAY DIFFRACTION99.3
2.32-2.360.28072940.24576156X-RAY DIFFRACTION99.29
2.36-2.40.2943320.23896088X-RAY DIFFRACTION99.01
2.4-2.450.27053110.21716089X-RAY DIFFRACTION99.44
2.45-2.510.24193570.20956094X-RAY DIFFRACTION99.28
2.51-2.560.27993130.20146145X-RAY DIFFRACTION99.45
2.56-2.630.26232980.19356151X-RAY DIFFRACTION99.29
2.63-2.70.23083300.18736144X-RAY DIFFRACTION99.66
2.7-2.780.24533150.18986154X-RAY DIFFRACTION99.45
2.78-2.870.22073310.20056129X-RAY DIFFRACTION99.54
2.87-2.970.23523220.20836153X-RAY DIFFRACTION99.63
2.97-3.090.26593610.21586144X-RAY DIFFRACTION99.68
3.09-3.230.25283330.21316199X-RAY DIFFRACTION99.66
3.23-3.40.21652690.19746218X-RAY DIFFRACTION99.83
3.4-3.610.21273910.18626158X-RAY DIFFRACTION99.79
3.61-3.890.21733100.18356259X-RAY DIFFRACTION99.83
3.89-4.280.18352980.14936288X-RAY DIFFRACTION99.89
4.28-4.90.16733270.13926295X-RAY DIFFRACTION99.94
4.9-6.180.18173350.15646347X-RAY DIFFRACTION99.97
6.18-49.40.15823350.15726512X-RAY DIFFRACTION98.86
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)
10.240099840623-0.03957671966570.07178794181380.08545156930740.10514872290.101629319296-0.120860357184-0.2042348212610.00503610341044-0.0577085130404-0.033728939347-0.0850026352102-0.255038911780.0490963490026-4.72580488258E-50.595575402512-0.189992314145-0.1182250087970.6798991364140.1708102305690.49060782248866.92573284790.93084437914113.546750648
20.293232514002-0.0126389148097-0.09027040483630.332687149420.009557611796980.1199880287780.151375317433-0.0963724235590.01513370657770.041752639801-0.2302034074030.1138805220720.272470425554-0.347890926091-0.01010510182770.545584215498-0.213996730140.02668399886850.6919749565290.01873313890520.45390718299331.6869458306-6.06846372518-18.2262520542
31.017440774770.450051922936-0.3361511792030.559399907475-0.1262168658130.4875896330020.0272782277988-0.0486998086883-0.236676101969-0.0372053818468-0.0635639688651-0.1623182245460.0958352967482-0.03500469788795.64900717174E-70.372215107046-0.03177069524990.01193995229940.3854120418060.04138826932120.41362613172266.34969001398.52104053669-31.2142359584
41.059361019590.557572337180.310826835050.3127832803380.2401438290540.4338663863540.214513189645-0.259125207170.2208343584510.158201925358-0.2415097175990.0768120427163-0.124375647433-0.098832310946-0.002596716270320.427344021721-0.08212131889740.07430381510170.5070083034770.02062959825260.40349611536852.850522855515.7858769898-20.0074206995
50.104614411589-0.272233434512-0.2609851669930.2282033927550.2850831790240.1195199870270.0543573782055-0.2011935993250.224749339631-0.1779981384840.0829736522969-0.181988821944-0.1492669416540.382257579933-8.06439571087E-60.548646359063-0.1349179623560.04985931215640.707910690492-0.02056544531830.57432358099246.190129296318.789024832913.9977026013
60.03419089814540.0522799695117-0.03356844080390.146590527791-0.05326772565630.0758523945798-0.4046160416290.299714646273-0.311824902632-0.3445572585710.05059848046010.1108044244220.518583430141-0.353183859708-0.1155978127980.757209246903-0.2257805608560.2465586721560.514170612417-0.2069872045950.70301089247315.8010535711-18.886637398217.4746173037
70.161222757457-0.04001177278140.148445608210.136354664740.009278999818290.170704896649-0.2650293747670.337263063658-0.434436215387-0.3979154423250.0793096479610.1721156013290.352914149554-0.3249260461-0.01428756331510.735310887592-0.2508855640270.1769057614610.586545522044-0.1768983257110.66574834037112.1261851413-15.853161761113.9120011188
80.7170248416010.350064096577-0.0707623356680.574060310375-0.3673284748410.286964555165-0.1362055922370.147528730540.219877954576-0.08047240704930.08717425696020.515557706499-0.124322495771-0.390849289803-2.15276747557E-50.437916598984-0.0148617365387-0.09060689257350.619584362510.0008995653235520.6593322961790.021342211282519.706668106423.2601021387
90.3993851505110.143109083020.08792989585190.513649630533-0.2236729810550.253398542543-0.0860102401289-0.0849006751633-0.009354220882260.1868237649120.01324042783940.137348406373-0.113020970111-0.22080878597-1.41932226244E-50.416423095721-0.04670826311570.0221880673630.480475854997-0.02596358171180.48474223511910.87327760759.8218189755434.3746854045
100.106005384123-0.119622914075-0.0635862983960.1204564777490.0665370410920.0284095287068-0.2549458354580.0168807865045-0.1543817182970.02688917828990.14144306949-0.1895687531880.02581792656840.000390824102983.19733076187E-50.436253292799-0.03790743442040.07392393280610.401555803866-0.05401249011590.52230642234630.5257221133-0.0023351376189827.5509444322
110.322509070365-0.168282913194-0.09806858713940.103076884075-0.03360215334280.3457091638980.111625432893-0.03447645210950.3687449398950.111486676104-0.00550150829095-0.356741279448-0.171784472440.0456629854774-4.0090943964E-60.4767511091080.0533043634882-0.01986781030060.3799190315-0.04880256333790.61468127757449.4839729491-5.3846012678738.5367842022
120.04705377133850.00322563191710.07492323418470.0128064437518-0.04533262397160.5449035492330.08252690291710.464123768042-0.288010589691-0.535528768339-0.4069307360250.455404430932-0.0590109863711-0.474659914078-0.5127319172291.417581063710.522305136359-0.4063426180420.925278238736-0.1441442396520.36419927308548.7227411377-34.84497182610.722451500983
130.09003759408670.0935086331089-0.06112721336720.0711588712989-0.05702252689850.0601297090762-0.1375978246620.174689406145-0.0662693719027-0.436991290939-0.04938311375890.288931870560.271730232389-0.17141395258-0.289759191451.265529664250.479469836939-0.6877216352491.00241235023-0.4342827183330.4806741405342.8619451098-44.0724234231.84932868332
140.212400897815-0.001575431750920.02141002790810.0942336009197-0.0485332213190.09837778777730.1510288343590.640379895040.148186145021-0.780890652336-0.3158476665930.210012648145-0.117141285679-0.0453371230061-0.1500882425021.493346305850.666024936492-0.6617639251720.951906067918-0.280480004855-0.048048186023547.4253620876-34.99515511495.35376404459
150.569194806859-0.383813481044-0.01116303194320.651856584850.06016543212640.6955013421450.193839556094-0.00814044403775-0.282858123068-0.193166075882-0.1267059934810.2176973484390.239763694598-0.116597720544-0.001986268032780.437649877153-0.00247492517582-0.09714861028880.323532409508-0.05309709972710.45206126371257.2511454139-49.624332280439.0086598702
160.0325024745173-0.00909649282668-0.007385520776220.0424766396385-0.0909977270520.08395148226970.01387463075640.2197848099-0.162543557147-0.282211649882-0.0343067822164-0.2425505948890.4070997862740.457697117063-1.23273397689E-50.5538197381150.140017502893-0.02420414265430.511934672321-0.0692579732620.47298432258873.4735366026-50.211003363630.1352571175
170.2245669253710.04914392555640.2402038929220.240254604641-0.1174569071690.3319674551950.1945012626940.2476208132180.0171402224872-0.52484860868-0.2328191779940.14682006385-0.0375077374011-0.0270134370362-0.0007619716619260.5540612998660.1185042961990.004381194308720.419805087873-0.0005989406007960.37997985226964.4326844136-34.935851573125.8881011048
180.0105557942513-0.02676859736140.06041103602610.0658858111096-0.06278692734740.1583019433320.176153927530.0298278535970.11809769978-0.40607143573-0.39874046818-0.07571537678560.04307614645420.519694882601-0.00330071686670.7640040697330.147620334406-0.09265103306580.5549977869380.05085396961580.489886937558.9359030904-18.97348594618.890755579
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 543 through 647 )BC543 - 647533 - 637
22chain 'C' and (resid 4 through 144 )CF4 - 1441 - 141
33chain 'C' and (resid 145 through 364 )CF145 - 364142 - 361
44chain 'C' and (resid 365 through 516 )CF365 - 516362 - 509
55chain 'C' and (resid 517 through 647 )CF517 - 647510 - 640
66chain 'A' and (resid 2 through 34 )AA2 - 341 - 33
77chain 'A' and (resid 35 through 144 )AA35 - 14434 - 143
88chain 'A' and (resid 145 through 375 )AA145 - 375144 - 374
99chain 'A' and (resid 376 through 498 )AA376 - 498375 - 497
1010chain 'A' and (resid 499 through 542 )AA499 - 542498 - 541
1111chain 'A' and (resid 543 through 647 )AA543 - 647542 - 646
1212chain 'B' and (resid 2 through 34 )BC2 - 341 - 33
1313chain 'B' and (resid 35 through 82 )BC35 - 8234 - 81
1414chain 'B' and (resid 83 through 144 )BC83 - 14482 - 143
1515chain 'B' and (resid 145 through 364 )BC145 - 364144 - 363
1616chain 'B' and (resid 365 through 412 )BC365 - 412364 - 402
1717chain 'B' and (resid 413 through 498 )BC413 - 498403 - 488
1818chain 'B' and (resid 499 through 542 )BC499 - 542489 - 532

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