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- PDB-9thv: Bacteriodes thetaiotamicron sulphatase BT1636_S77C in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9thv
TitleBacteriodes thetaiotamicron sulphatase BT1636_S77C in complex with Chromate Ions
ComponentsArylsulfatase
KeywordsSUGAR BINDING PROTEIN / Carbohydrate / Sulphatase / Complex / Inhibitor
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Chromate / Arylsulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTomlinson, C.W.E. / Cartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Fluorogenic Coupled Assays Reveal Catalytic Properties, Inhibition Constants and Cellular Location of Mucin-Active Carbohydrate Sulfatases.
Authors: Tomlinson, C.W.E. / Bergers, M.D. / Bolam, D.N. / Luis, A.S. / Cartmell, A. / Armstrong, Z.
History
DepositionDec 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 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: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3044
Polymers58,0291
Non-polymers2743
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-5 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.651, 87.594, 103.322
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arylsulfatase


Mass: 58029.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_1636 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A789
#2: Chemical ChemComp-CQ4 / Chromate / Dioxido(dioxo)chromium


Mass: 115.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CrO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 300 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 40% MPD, 5% PEG 8000, 100 mM Sodium Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→66.81 Å / Num. obs: 75194 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Rrim(I) all: 0.116 / Χ2: 0.36 / Net I/σ(I): 10
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
9-66.8111.30.03169.56030.9990.0130.0331.24
1.7-1.7314.12.0810.439170.6580.8322.2420.08

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.105)refinement
REFMAC5.8.0431 (refmacat 0.4.105)refinement
Aimlessdata scaling
DIMPLEphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→66.81 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.965 / SU B: 6.187 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 3869 5.15 %RANDOM
Rwork0.1528 71250 --
all0.155 ---
obs-75119 100 %-
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: 32.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.269 Å2-0 Å20 Å2
2--0.423 Å2-0 Å2
3----0.693 Å2
Refinement stepCycle: LAST / Resolution: 1.7→66.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 14 300 4176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124012
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163637
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.8285433
X-RAY DIFFRACTIONr_angle_other_deg0.5731.778416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0365486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.177517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29510662
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.31110201
X-RAY DIFFRACTIONr_chiral_restr0.0830.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02945
X-RAY DIFFRACTIONr_nbd_refined0.2050.2750
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.23385
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21936
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1030.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.25
X-RAY DIFFRACTIONr_nbd_other0.2430.29
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.210
X-RAY DIFFRACTIONr_mcbond_it6.55531938
X-RAY DIFFRACTIONr_mcbond_other6.54831938
X-RAY DIFFRACTIONr_mcangle_it9.0985.3942426
X-RAY DIFFRACTIONr_mcangle_other9.0995.3952427
X-RAY DIFFRACTIONr_scbond_it8.6363.3122074
X-RAY DIFFRACTIONr_scbond_other8.6343.3132075
X-RAY DIFFRACTIONr_scangle_it12.2325.9363007
X-RAY DIFFRACTIONr_scangle_other12.235.9373008
X-RAY DIFFRACTIONr_lrange_it15.51529.6544558
X-RAY DIFFRACTIONr_lrange_other15.16529.1354502
X-RAY DIFFRACTIONr_rigid_bond_restr3.68437649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.7-1.7440.3972740.40252030.40154770.8760.870.399
1.744-1.7920.3952330.38351120.38453450.8780.890.382
1.792-1.8440.3572310.34849690.34852000.9080.9130.345
1.844-1.9010.2952830.29847840.29850670.940.9430.294
1.901-1.9630.2782390.23646720.23849110.9480.9650.227
1.963-2.0320.2342370.18345020.18547390.9670.9780.168
2.032-2.1080.2272270.15643610.15945880.9680.9850.139
2.108-2.1940.212560.14641840.14944400.9730.9870.126
2.194-2.2920.1712410.12939970.13242380.9810.990.109
2.292-2.4030.162210.11238660.11540870.9840.9930.093
2.403-2.5330.1681930.11336540.11638470.9830.9930.094
2.533-2.6870.1791980.11434910.11736890.9810.9930.095
2.687-2.8720.1811940.11932880.12234820.9810.9920.103
2.872-3.1010.181770.13830440.1432210.9810.990.123
3.101-3.3970.1861260.14628690.14829950.9790.9890.134
3.397-3.7960.1661330.12725810.12827140.9850.9920.118
3.796-4.3810.1511380.122790.10324170.9870.9940.097
4.381-5.360.1431130.11519500.11720630.990.9940.114
5.36-7.5560.2131030.17315260.17516290.9790.9880.167
7.556-66.810.196520.1759180.1769700.9790.9790.185

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