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- PDB-9hh2: Crystal structure of the family S1_19 carrageenan sulfatase ZgCgs... -

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Basic information

Entry
Database: PDB / ID: 9hh2
TitleCrystal structure of the family S1_19 carrageenan sulfatase ZgCgsA from Zobellia galactanivorans in complex with hybrid a-i-neocarratetraose
ComponentsSulfatase, family S1-19
KeywordsHYDROLASE / sulfatase / S1_19 / carrageenan / covalent intermediate / substrate specificity / complex / oligosaccharide
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / arylsulfatase activity
Similarity search - Function
: / Sulfatases signature 2. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
BROMIDE ION / Sulfatase, family S1-19
Similarity search - Component
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsChevenier, A. / Czjzek, M. / Michel, G. / Ficko-Blean, E.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR- 22-CE11-0025-01 France
CitationJournal: Carbohydr Polym / Year: 2025
Title: Structure, function and catalytic mechanism of the carrageenan-sulfatases from the marine bacterium Zobellia galactanivorans Dsij T.
Authors: Chevenier, A. / Fanuel, M. / Sokolova, E. / Mico Latorre, D. / Jouanneau, D. / Jeudy, A. / Prechoux, A. / Zuhlke, M.K. / Bartel, J. / Becher, D. / Czjzek, M. / Ropartz, D. / Michel, G. / Ficko-Blean, E.
History
DepositionNov 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: 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, family S1-19
B: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,73027
Polymers109,5572
Non-polymers3,17325
Water17,961997
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-63 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.630, 96.190, 106.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Sulfatase, family S1-19


Mass: 54778.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (bacteria) / Gene: zobellia_3145 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G0L000, Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases
#2: Polysaccharide 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O- ...3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 870.737 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2112h-1b_1-5_4*OSO/3=O/3=O][a2112h-1a_1-5_3-6_2*OSO/3=O/3=O][a2112h-1b_1-5]/1-2-3-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][<C12O15S2>]{[(1+1)][b-D-Galp]{[(3+1)]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1020 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BR / BROMIDE ION


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


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 997 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane pH 7.5, 0.1 M NaBr, 8% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.58→43.63 Å / Num. obs: 134822 / % possible obs: 99.96 % / Redundancy: 15 % / CC1/2: 1 / Net I/σ(I): 21.07
Reflection shellResolution: 1.58→1.636 Å / Num. unique obs: 13332 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→43.63 Å / SU ML: 0.1859 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.2788
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1768 6743 5 %
Rwork0.152 128107 -
obs0.1533 134822 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.38 Å2
Refinement stepCycle: LAST / Resolution: 1.58→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7409 0 163 997 8569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00587826
X-RAY DIFFRACTIONf_angle_d0.838410642
X-RAY DIFFRACTIONf_chiral_restr0.05441116
X-RAY DIFFRACTIONf_plane_restr0.00941376
X-RAY DIFFRACTIONf_dihedral_angle_d13.54972932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.31962190.2854175X-RAY DIFFRACTION98.85
1.6-1.620.30632240.27264239X-RAY DIFFRACTION99.96
1.62-1.640.27762210.25894209X-RAY DIFFRACTION99.98
1.64-1.660.272220.24994215X-RAY DIFFRACTION100
1.66-1.680.29112230.2274233X-RAY DIFFRACTION99.96
1.68-1.70.24972220.21444218X-RAY DIFFRACTION100
1.7-1.730.2412240.19574258X-RAY DIFFRACTION100
1.73-1.750.24282230.18744234X-RAY DIFFRACTION100
1.75-1.780.20762230.17714242X-RAY DIFFRACTION100
1.78-1.810.22692230.17014230X-RAY DIFFRACTION100
1.81-1.840.20872240.16464253X-RAY DIFFRACTION100
1.84-1.870.17712230.15824240X-RAY DIFFRACTION100
1.87-1.910.182230.1524251X-RAY DIFFRACTION100
1.91-1.950.17632230.15474224X-RAY DIFFRACTION99.98
1.95-1.990.17252240.15154256X-RAY DIFFRACTION100
1.99-2.040.18812230.14494243X-RAY DIFFRACTION100
2.04-2.090.16892250.13554277X-RAY DIFFRACTION100
2.09-2.140.16562240.13544262X-RAY DIFFRACTION100
2.14-2.210.18562240.13944251X-RAY DIFFRACTION100
2.21-2.280.16742260.14064283X-RAY DIFFRACTION100
2.28-2.360.16682230.14224251X-RAY DIFFRACTION100
2.36-2.450.1862250.1414260X-RAY DIFFRACTION100
2.45-2.570.16962250.14974287X-RAY DIFFRACTION100
2.57-2.70.16862260.1454295X-RAY DIFFRACTION100
2.7-2.870.1682270.14534296X-RAY DIFFRACTION99.96
2.87-3.090.17552260.14494311X-RAY DIFFRACTION99.96
3.09-3.40.16092280.13684330X-RAY DIFFRACTION100
3.4-3.890.15032300.12744354X-RAY DIFFRACTION100
3.89-4.910.13352300.12514384X-RAY DIFFRACTION99.98
4.91-43.630.19882400.19274546X-RAY DIFFRACTION99.42

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