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- PDB-9s88: Amuc0121_S1_15 in complex with O6 sulfated Lewis A antigen (6'S-LeA) -

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Basic information

Entry
Database: PDB / ID: 9s88
TitleAmuc0121_S1_15 in complex with O6 sulfated Lewis A antigen (6'S-LeA)
ComponentsSulfatase
KeywordsHYDROLASE / Carbohydrate sulfatase / mucin / Akkermansia muciniphila / Sulfation
Function / homology
Function and homology information


: / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BROMIDE ION / IODIDE ION / Sulfatase
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsDey, D. / Cartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust225897/Z/22/Z United Kingdom
CitationJournal: To Be Published
Title: The role of Akkermansia muciniphila sulfatases in colonic mucin utilisation
Authors: Dey, D. / Salman, N.D. / Tomlinson, C.W.E. / Gugel, S. / Chunsheng, J. / Raba, G. / Nilsson, M. / McIver, Z. / Simpkin, A. / Davy, M. / Rigden, D.J. / Czjzek, M. / Byrne, D.P. / Case, A. / ...Authors: Dey, D. / Salman, N.D. / Tomlinson, C.W.E. / Gugel, S. / Chunsheng, J. / Raba, G. / Nilsson, M. / McIver, Z. / Simpkin, A. / Davy, M. / Rigden, D.J. / Czjzek, M. / Byrne, D.P. / Case, A. / Baumann, C. / Wright, G.S.A. / van der Post, S. / Martens, E.C. / Yates, E.A. / Davey, L. / Luis, A.S. / Cartmell, A.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfatase
B: Sulfatase
C: Sulfatase
D: Sulfatase
E: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,31623
Polymers272,3345
Non-polymers3,98118
Water6,539363
1
A: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3235
Polymers54,4671
Non-polymers8564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1163
Polymers54,4671
Non-polymers6502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2765
Polymers54,4671
Non-polymers8094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1964
Polymers54,4671
Non-polymers7303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4036
Polymers54,4671
Non-polymers9365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.04, 64.15, 151.36
Angle α, β, γ (deg.)90, 104.88, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
32A
42C
53A
63D
74A
84E
95B
105C
116B
126D
137B
147E
158C
168D
179C
189E
1910D
2010E

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALARGARGAA26 - 5112 - 487
211VALVALARGARGBB26 - 5112 - 487
322VALVALARGARGAA26 - 5112 - 487
422VALVALARGARGCC26 - 5112 - 487
533VALVALARGARGAA26 - 5112 - 487
633VALVALARGARGDD26 - 5112 - 487
744THRTHRARGARGAA25 - 5111 - 487
844THRTHRARGARGEE25 - 5111 - 487
955VALVALARGARGBB26 - 5112 - 487
1055VALVALARGARGCC26 - 5112 - 487
1166VALVALARGARGBB26 - 5112 - 487
1266VALVALARGARGDD26 - 5112 - 487
1377VALVALARGARGBB26 - 5112 - 487
1477VALVALARGARGEE26 - 5112 - 487
1588VALVALSERSERCC26 - 5122 - 488
1688VALVALSERSERDD26 - 5122 - 488
1799VALVALSERSERCC26 - 5122 - 488
1899VALVALSERSEREE26 - 5122 - 488
191010VALVALSERSERDD26 - 5122 - 488
201010VALVALSERSEREE26 - 5122 - 488

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20

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Components

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Protein / Sugars , 2 types, 10 molecules ABCDE

#1: Protein
Sulfatase


Mass: 54466.852 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_0121 / Production host: Escherichia coli (E. coli) / References: UniProt: B2ULS2
#2: Polysaccharide
6-O-sulfo-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 609.553 Da / Num. of mol.: 5 / Source method: obtained synthetically
DescriptorTypeProgram
DGalp[6S]b1-3[LFucpa1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5_6*OSO/3=O/3=O][a1221m-1a_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][b-D-Galp6SO3]{}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 376 molecules

#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus B1: 30 % Precipitant mix 1 (40% v/v PEG 500 MME; 20 % w/v PEG 20000) 0.1 M Buffer system 1 pH 6.5 (Imidazole; MES monohydrate acid) 0.09 M Halogens (0.3M Sodium fluoride; 0.3M ...Details: Morpheus B1: 30 % Precipitant mix 1 (40% v/v PEG 500 MME; 20 % w/v PEG 20000) 0.1 M Buffer system 1 pH 6.5 (Imidazole; MES monohydrate acid) 0.09 M Halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide) 36 mgml Amuc0121_C78S ,Co-crystallised with 1 mM 6S-LeA and soaked with ~5 mM ~72h

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.92→58.75 Å / Num. obs: 1313104 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.991 / Net I/σ(I): 9.3
Reflection shellResolution: 1.92→1.95 Å / Num. unique obs: 56063 / CC1/2: 0.421

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→57.856 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.616 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.177 / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.236 9703 5.056 %
Rwork0.2076 182211 -
all0.209 --
obs-191914 99.367 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.568 Å2
Baniso -1Baniso -2Baniso -3
1-2.339 Å2-0 Å20.88 Å2
2--0.332 Å2-0 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 1.92→57.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18886 0 213 363 19462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01219767
X-RAY DIFFRACTIONr_bond_other_d0.0010.01618816
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.82826750
X-RAY DIFFRACTIONr_angle_other_deg0.5381.78543620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47952484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.555134
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.211510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.671103430
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.21410848
X-RAY DIFFRACTIONr_chiral_restr0.0720.22869
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223241
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024325
X-RAY DIFFRACTIONr_nbd_refined0.2190.23645
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.216810
X-RAY DIFFRACTIONr_nbtor_refined0.1740.29549
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.29990
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2631
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3330.232
X-RAY DIFFRACTIONr_nbd_other0.2420.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.220
X-RAY DIFFRACTIONr_mcbond_it3.0833.7299888
X-RAY DIFFRACTIONr_mcbond_other3.0833.739889
X-RAY DIFFRACTIONr_mcangle_it4.1156.69212388
X-RAY DIFFRACTIONr_mcangle_other4.1156.69312389
X-RAY DIFFRACTIONr_scbond_it3.8864.0919879
X-RAY DIFFRACTIONr_scbond_other3.8854.0919880
X-RAY DIFFRACTIONr_scangle_it5.7787.32714362
X-RAY DIFFRACTIONr_scangle_other5.7787.32714363
X-RAY DIFFRACTIONr_lrange_it6.85935.64621312
X-RAY DIFFRACTIONr_lrange_other6.85935.61121274
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.0516620
X-RAY DIFFRACTIONr_ncsr_local_group_20.0630.0516586
X-RAY DIFFRACTIONr_ncsr_local_group_30.0610.0516578
X-RAY DIFFRACTIONr_ncsr_local_group_40.0520.0516703
X-RAY DIFFRACTIONr_ncsr_local_group_50.0570.0516327
X-RAY DIFFRACTIONr_ncsr_local_group_60.0590.0516259
X-RAY DIFFRACTIONr_ncsr_local_group_70.0590.0516233
X-RAY DIFFRACTIONr_ncsr_local_group_80.0520.0516406
X-RAY DIFFRACTIONr_ncsr_local_group_90.0640.0516341
X-RAY DIFFRACTIONr_ncsr_local_group_100.0610.0516351
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.058640.0501
12BX-RAY DIFFRACTIONLocal ncs0.058640.0501
23AX-RAY DIFFRACTIONLocal ncs0.063080.0501
24CX-RAY DIFFRACTIONLocal ncs0.063080.0501
35AX-RAY DIFFRACTIONLocal ncs0.061250.0501
36DX-RAY DIFFRACTIONLocal ncs0.061250.0501
47AX-RAY DIFFRACTIONLocal ncs0.052460.0501
48EX-RAY DIFFRACTIONLocal ncs0.052460.0501
59BX-RAY DIFFRACTIONLocal ncs0.056550.0501
510CX-RAY DIFFRACTIONLocal ncs0.056550.0501
611BX-RAY DIFFRACTIONLocal ncs0.059060.0501
612DX-RAY DIFFRACTIONLocal ncs0.059060.0501
713BX-RAY DIFFRACTIONLocal ncs0.059070.0501
714EX-RAY DIFFRACTIONLocal ncs0.059070.0501
815CX-RAY DIFFRACTIONLocal ncs0.051760.0501
816DX-RAY DIFFRACTIONLocal ncs0.051760.0501
917CX-RAY DIFFRACTIONLocal ncs0.063640.0501
918EX-RAY DIFFRACTIONLocal ncs0.063640.0501
1019DX-RAY DIFFRACTIONLocal ncs0.061020.0501
1020EX-RAY DIFFRACTIONLocal ncs0.061020.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.9650.3437000.34912603X-RAY DIFFRACTION93.7491
1.965-2.0190.3276710.32313081X-RAY DIFFRACTION99.4144
2.019-2.0770.3197000.30412726X-RAY DIFFRACTION99.5256
2.077-2.1410.3096690.28212362X-RAY DIFFRACTION99.6482
2.141-2.2110.2946300.26211997X-RAY DIFFRACTION99.7315
2.211-2.2890.2796460.23711605X-RAY DIFFRACTION99.8045
2.289-2.3750.2546130.22811195X-RAY DIFFRACTION99.814
2.375-2.4720.2645990.21310759X-RAY DIFFRACTION99.8769
2.472-2.5810.2615360.21410406X-RAY DIFFRACTION99.9726
2.581-2.7070.2575060.2119951X-RAY DIFFRACTION99.9522
2.707-2.8530.2565190.2059427X-RAY DIFFRACTION99.9899
2.853-3.0260.2444960.1968956X-RAY DIFFRACTION99.9788
3.026-3.2340.2214480.2048428X-RAY DIFFRACTION99.9212
3.234-3.4920.234110.2087869X-RAY DIFFRACTION100
3.492-3.8240.223670.2017299X-RAY DIFFRACTION99.9739
3.824-4.2730.1983440.176592X-RAY DIFFRACTION99.9856
4.273-4.930.1782880.1515843X-RAY DIFFRACTION99.9837
4.93-6.0270.1872450.1754969X-RAY DIFFRACTION99.9425
6.027-8.4780.1782100.1593879X-RAY DIFFRACTION99.9023
8.478-57.8560.1911050.1752263X-RAY DIFFRACTION99.4123

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