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- PDB-9s8f: Amuc1755_S1_16 in complex with D-Galactose -

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Basic information

Entry
Database: PDB / ID: 9s8f
TitleAmuc1755_S1_16 in complex with D-Galactose
ComponentsSulfatase
KeywordsHYDROLASE / Carbohydrate sulfatase / mucin / Akkermansia muciniphila / Sulfation
Function / homology: / arylsulfatase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / beta-D-galactopyranose / Sulfatase
Function and homology information
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1143
Polymers59,8941
Non-polymers2202
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint2 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.08, 143.08, 50.41
Angle α, β, γ (deg.)90, 90, 120
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Sulfatase


Mass: 59893.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_1755 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UML7
#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.: 1 / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.6 M Sodium Malonate Amuc1755 2,75 mg/ml 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 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→71.54 Å / Num. obs: 344730 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 28425 / CC1/2: 0.666

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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: 2.1→71.54 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.148 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.189 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2072 1753 5.048 %
Rwork0.1662 32976 -
all0.168 --
obs-34729 99.994 %
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: 37.145 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.275 Å2-0 Å2
2---0.55 Å20 Å2
3---1.785 Å2
Refinement stepCycle: LAST / Resolution: 2.1→71.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 13 116 4343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124385
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164079
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.8315947
X-RAY DIFFRACTIONr_angle_other_deg0.5891.7769417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.772531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66410741
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.610209
X-RAY DIFFRACTIONr_chiral_restr0.0820.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
X-RAY DIFFRACTIONr_nbd_refined0.2130.2870
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.23785
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22145
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2161
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0710.210
X-RAY DIFFRACTIONr_nbd_other0.210.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.24
X-RAY DIFFRACTIONr_mcbond_it2.7573.4492157
X-RAY DIFFRACTIONr_mcbond_other2.7573.4492158
X-RAY DIFFRACTIONr_mcangle_it3.9016.1982705
X-RAY DIFFRACTIONr_mcangle_other3.9016.1982706
X-RAY DIFFRACTIONr_scbond_it4.0593.8852228
X-RAY DIFFRACTIONr_scbond_other4.0593.8862229
X-RAY DIFFRACTIONr_scangle_it6.2646.9183242
X-RAY DIFFRACTIONr_scangle_other6.2636.9193243
X-RAY DIFFRACTIONr_lrange_it7.3133.0954872
X-RAY DIFFRACTIONr_lrange_other7.31432.9974865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.3271350.2572386X-RAY DIFFRACTION100
2.155-2.2140.2621200.2342384X-RAY DIFFRACTION100
2.214-2.2780.2841360.2272276X-RAY DIFFRACTION100
2.278-2.3480.2821170.2072204X-RAY DIFFRACTION100
2.348-2.4250.2381130.1952177X-RAY DIFFRACTION100
2.425-2.510.2541110.1882107X-RAY DIFFRACTION100
2.51-2.6040.2141220.1991981X-RAY DIFFRACTION100
2.604-2.710.2421270.1981932X-RAY DIFFRACTION100
2.71-2.8310.211920.1821870X-RAY DIFFRACTION100
2.831-2.9690.253760.1911817X-RAY DIFFRACTION99.9472
2.969-3.1290.23750.1711720X-RAY DIFFRACTION100
3.129-3.3180.177750.1671617X-RAY DIFFRACTION100
3.318-3.5470.236690.1581524X-RAY DIFFRACTION100
3.547-3.830.174790.1361413X-RAY DIFFRACTION100
3.83-4.1950.139730.1221323X-RAY DIFFRACTION100
4.195-4.6880.125670.1071168X-RAY DIFFRACTION100
4.688-5.4090.174450.111061X-RAY DIFFRACTION100
5.409-6.6160.203470.154901X-RAY DIFFRACTION100
6.616-9.3160.169400.156709X-RAY DIFFRACTION100
9.316-71.540.252340.245406X-RAY DIFFRACTION100

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