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- PDB-9hh4: Crystal structure of the family S1_19 carrageenan sulfatase ZgCgs... -

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Basic information

Entry
Database: PDB / ID: 9hh4
TitleCrystal structure of the family S1_19 carrageenan sulfatase ZgCgsA from Zobellia galactanivorans in complex with hybrid b-k-neocarratetraose
ComponentsSulfatase, family S1-19
KeywordsHYDROLASE / sulfatase / S1_19 / carrageenan / covalent intermediate / substrate specificity / complex
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: 1.92 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 21, 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)224,46552
Polymers219,1144
Non-polymers5,35148
Water27,3291517
1
A: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,32917
Polymers54,7781
Non-polymers1,55016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,09512
Polymers54,7781
Non-polymers1,31611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,94611
Polymers54,7781
Non-polymers1,16810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,09512
Polymers54,7781
Non-polymers1,31611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Sulfatase, family S1-19
B: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,42429
Polymers109,5572
Non-polymers2,86727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-112 kcal/mol
Surface area33880 Å2
MethodPISA
6
D: Sulfatase, family S1-19
hetero molecules

C: Sulfatase, family S1-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,04123
Polymers109,5572
Non-polymers2,48421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area6960 Å2
ΔGint-82 kcal/mol
Surface area33400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.230, 197.600, 75.020
Angle α, β, γ (deg.)90.00, 99.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Sulfatase, family S1-19


Mass: 54778.480 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: Polysaccharide
3,6-anhydro-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D- ...3,6-anhydro-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 710.611 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2112h-1b_1-5_4*OSO/3=O/3=O][a2112h-1a_1-5_3-6][a2112h-1b_1-5]/1-2-3-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0

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Non-polymers , 5 types, 1561 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: Br
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1517 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane pH 7.5, 0.1 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: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.92→36.57 Å / Num. obs: 159811 / % possible obs: 99.37 % / Redundancy: 8.8 % / CC1/2: 0.999 / Net I/σ(I): 15.27
Reflection shellResolution: 1.92→1.99 Å / Num. unique obs: 15573 / CC1/2: 0.694

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→36.57 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 7985 5 %
Rwork0.1669 --
obs0.1689 159702 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→36.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14853 0 267 1517 16637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915533
X-RAY DIFFRACTIONf_angle_d1.0121085
X-RAY DIFFRACTIONf_dihedral_angle_d15.95786
X-RAY DIFFRACTIONf_chiral_restr0.0622197
X-RAY DIFFRACTIONf_plane_restr0.0142728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.36882510.34944745X-RAY DIFFRACTION94
1.95-1.970.34442660.3195045X-RAY DIFFRACTION99
1.97-1.990.33452620.29564975X-RAY DIFFRACTION99
1.99-2.020.2932660.27035049X-RAY DIFFRACTION99
2.02-2.040.2792650.23875037X-RAY DIFFRACTION99
2.04-2.070.27862680.22575072X-RAY DIFFRACTION99
2.07-2.10.25922620.21244986X-RAY DIFFRACTION99
2.1-2.130.25362660.20545088X-RAY DIFFRACTION99
2.13-2.170.24852640.19635021X-RAY DIFFRACTION99
2.17-2.20.2522690.19855106X-RAY DIFFRACTION100
2.2-2.240.2572660.19845048X-RAY DIFFRACTION100
2.24-2.280.23252650.2015046X-RAY DIFFRACTION100
2.28-2.320.23072670.19095073X-RAY DIFFRACTION99
2.32-2.370.21422650.18445025X-RAY DIFFRACTION100
2.37-2.420.21642680.17835093X-RAY DIFFRACTION100
2.42-2.480.23872680.17585094X-RAY DIFFRACTION100
2.48-2.540.22662640.17045025X-RAY DIFFRACTION100
2.54-2.610.2212680.16795083X-RAY DIFFRACTION100
2.61-2.690.21752660.16335073X-RAY DIFFRACTION100
2.69-2.770.20292680.16375103X-RAY DIFFRACTION100
2.77-2.870.20292670.15875059X-RAY DIFFRACTION100
2.87-2.990.21362690.1645109X-RAY DIFFRACTION100
2.99-3.120.2332680.16525094X-RAY DIFFRACTION100
3.12-3.290.19732660.15565061X-RAY DIFFRACTION100
3.29-3.490.19672690.1475103X-RAY DIFFRACTION100
3.49-3.760.16962680.14045100X-RAY DIFFRACTION100
3.76-4.140.17432690.13675109X-RAY DIFFRACTION100
4.14-4.740.16642690.12465100X-RAY DIFFRACTION100
4.74-5.970.17432680.15685110X-RAY DIFFRACTION100
5.97-36.570.19732680.17245085X-RAY DIFFRACTION98

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