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- PDB-9s7x: Amuc0121_S1_15 in complex with D-Galactose -

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Basic information

Entry
Database: PDB / ID: 9s7x
TitleAmuc0121_S1_15 in complex with D-Galactose
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
2-[2-(2-ethoxyethoxy)ethoxy]ethanol / beta-D-galactopyranose / Sulfatase
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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

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Assembly

Deposited unit
A: Sulfatase
B: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6177
Polymers108,9982
Non-polymers6195
Water10,737596
1
A: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8974
Polymers54,4991
Non-polymers3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7193
Polymers54,4991
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.51, 91.49, 162.08
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sulfatase


Mass: 54498.918 Da / Num. of mol.: 2
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: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-FWN / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Morpheus H12- 37.5 % Precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350), 0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE), 0.1 M amino acids (0.2M DL-Glutamic acid monohydrate; ...Details: Morpheus H12- 37.5 % Precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350), 0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE), 0.1 M amino acids (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine) 36 mg/ml Amuc0121 with 100 mM D-Galactose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→61.607 Å / Num. obs: 141184 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 1.56→1.59 Å / Num. unique obs: 6959 / CC1/2: 0.589

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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: 1.56→61.607 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.873 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1843 7026 4.98 %
Rwork0.1379 134059 -
all0.14 --
obs-141085 99.975 %
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: 30.965 Å2
Baniso -1Baniso -2Baniso -3
1--1.064 Å20 Å20 Å2
2--1.906 Å2-0 Å2
3----0.843 Å2
Refinement stepCycle: LAST / Resolution: 1.56→61.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7525 0 38 596 8159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127915
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167580
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.8210709
X-RAY DIFFRACTIONr_angle_other_deg0.5811.78517556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61251009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.7550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.191101381
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.93410338
X-RAY DIFFRACTIONr_chiral_restr0.0840.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029392
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021748
X-RAY DIFFRACTIONr_nbd_refined0.2150.21454
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.26704
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23798
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2483
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1020.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.070.210
X-RAY DIFFRACTIONr_nbd_other0.2370.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.213
X-RAY DIFFRACTIONr_mcbond_it6.5972.8243988
X-RAY DIFFRACTIONr_mcbond_other6.5932.8243988
X-RAY DIFFRACTIONr_mcangle_it9.0065.0845013
X-RAY DIFFRACTIONr_mcangle_other9.0085.0865014
X-RAY DIFFRACTIONr_scbond_it8.8263.1793927
X-RAY DIFFRACTIONr_scbond_other8.8253.183928
X-RAY DIFFRACTIONr_scangle_it12.4555.6555696
X-RAY DIFFRACTIONr_scangle_other12.4545.6555697
X-RAY DIFFRACTIONr_lrange_it15.5628.2248771
X-RAY DIFFRACTIONr_lrange_other15.12127.7298646
X-RAY DIFFRACTIONr_rigid_bond_restr3.6315495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.56-1.6010.2734930.24598460.247103440.9630.97499.95170.243
1.601-1.6440.265010.22695650.227100670.9630.97899.99010.219
1.644-1.6920.2445150.19292860.19598020.9690.98599.98980.182
1.692-1.7440.2234710.16790190.1794900.9730.9881000.153
1.744-1.8010.2054580.14688060.14992640.9760.9911000.131
1.801-1.8640.1844630.11684690.1289320.9810.9941000.1
1.864-1.9350.194250.11481790.11886060.9790.99399.97680.099
1.935-2.0140.1744120.11579240.11883370.980.99399.9880.102
2.014-2.1030.1933840.12875870.13179720.9780.99299.98740.116
2.103-2.2050.1783560.12372730.12676290.9810.9931000.114
2.205-2.3250.1753500.12169250.12372760.9820.99399.98630.114
2.325-2.4650.1743600.11665920.11969520.9830.9931000.111
2.465-2.6350.1853250.12661410.12964670.9810.99199.98450.124
2.635-2.8460.1923100.13357490.13660600.9760.9999.98350.135
2.846-3.1170.1922870.14253110.14555980.9770.9881000.15
3.117-3.4840.1852710.15548310.15751030.980.98799.98040.168
3.484-4.0210.1562360.13542820.13645200.9860.9999.95570.156
4.021-4.9190.1481720.11536820.11638570.990.99499.92220.141
4.919-6.9340.1721390.15829060.15930470.9860.99199.93440.189
6.934-61.6070.218980.15816860.16117950.9740.98899.38720.204

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