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- PDB-9hh3: Structure of the apo ZgCgsA carrageenan-sulfatase (S1_19) from th... -

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Basic information

Entry
Database: PDB / ID: 9hh3
TitleStructure of the apo ZgCgsA carrageenan-sulfatase (S1_19) from the marine bacterium Zobellia galactanivorans
ComponentsSulfatase, family S1-19
KeywordsHYDROLASE / Bacterial metabolism / carrageenan / sulfatases / formylglycine / S1_19
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: 2.26 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
C: Sulfatase, family S1-19
D: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,70443
Polymers218,8584
Non-polymers1,84639
Water8,215456
1
A: Sulfatase, family S1-19
B: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,48524
Polymers109,4292
Non-polymers1,05622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-143 kcal/mol
Surface area33520 Å2
MethodPISA
2
D: Sulfatase, family S1-19
hetero molecules

C: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,21919
Polymers109,4292
Non-polymers79017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4800 Å2
ΔGint-112 kcal/mol
Surface area33060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.800, 199.150, 75.350
Angle α, β, γ (deg.)90.000, 99.330, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Sulfatase, family S1-19


Mass: 54714.480 Da / Num. of mol.: 4
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: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.56 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bis-Tris Propane pH 7.5, 0.2 M NaBr, 10 % 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: Apr 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.26→49.36 Å / Num. obs: 99086 / % possible obs: 99.62 % / Redundancy: 7.7 % / Biso Wilson estimate: 48.63 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1079 / Rpim(I) all: 0.0417 / Rrim(I) all: 0.1159 / Net I/σ(I): 13.37
Reflection shellResolution: 2.264→2.345 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.321 / Num. unique obs: 9564 / CC1/2: 0.564 / CC star: 0.849 / Rpim(I) all: 0.518 / % possible all: 96.66

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→49.36 Å / SU ML: 0.3278 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 4954 5 %
Rwork0.195 94109 -
obs0.1975 99063 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.55 Å2
Refinement stepCycle: LAST / Resolution: 2.26→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14617 0 39 456 15112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007715043
X-RAY DIFFRACTIONf_angle_d0.947420467
X-RAY DIFFRACTIONf_chiral_restr0.05822118
X-RAY DIFFRACTIONf_plane_restr0.0092704
X-RAY DIFFRACTIONf_dihedral_angle_d14.21795387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.290.37111510.32412851X-RAY DIFFRACTION90.2
2.29-2.320.31421650.29913133X-RAY DIFFRACTION99.94
2.32-2.350.31731630.28213101X-RAY DIFFRACTION99.97
2.35-2.370.30441670.27593182X-RAY DIFFRACTION99.94
2.37-2.410.34051640.27093111X-RAY DIFFRACTION99.91
2.41-2.440.29471670.27273166X-RAY DIFFRACTION100
2.44-2.470.34711660.27133149X-RAY DIFFRACTION100
2.47-2.510.31361640.26463124X-RAY DIFFRACTION100
2.51-2.550.29211660.24793146X-RAY DIFFRACTION100
2.55-2.590.29361640.2383121X-RAY DIFFRACTION100
2.59-2.640.30541660.21863157X-RAY DIFFRACTION100
2.64-2.680.26571650.21363140X-RAY DIFFRACTION99.97
2.68-2.740.28911650.21123129X-RAY DIFFRACTION100
2.74-2.790.26111660.22033150X-RAY DIFFRACTION99.97
2.79-2.850.26571650.21483147X-RAY DIFFRACTION100
2.85-2.920.28751670.22273158X-RAY DIFFRACTION100
2.92-2.990.28181650.22963138X-RAY DIFFRACTION100
2.99-3.070.28471660.23343161X-RAY DIFFRACTION100
3.07-3.160.28391640.22693113X-RAY DIFFRACTION99.97
3.16-3.270.26451660.21463160X-RAY DIFFRACTION99.97
3.27-3.380.27981660.21553142X-RAY DIFFRACTION99.97
3.38-3.520.25411650.20313145X-RAY DIFFRACTION99.97
3.52-3.680.2361670.19013165X-RAY DIFFRACTION99.94
3.68-3.870.22091650.18163145X-RAY DIFFRACTION99.94
3.87-4.110.21271660.163140X-RAY DIFFRACTION100
4.11-4.430.20851670.14833170X-RAY DIFFRACTION100
4.43-4.880.17261650.14443141X-RAY DIFFRACTION99.88
4.88-5.580.2091660.16533157X-RAY DIFFRACTION99.97
5.58-7.030.23781670.18273173X-RAY DIFFRACTION100
7.03-49.360.22161680.173194X-RAY DIFFRACTION99.61

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