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- PDB-9s03: X-ray structure of the S1_11 sulfatase MfFcsGS1_11 from Marinifle... -

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Basic information

Entry
Database: PDB / ID: 9s03
TitleX-ray structure of the S1_11 sulfatase MfFcsGS1_11 from Mariniflexile fucanivorans
ComponentsPutative sulfatase
KeywordsHYDROLASE / S1_11 sulfatase Mariniflexile fucanivorans Marine bacteria
Function / homology
Function and homology information


N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Alkaline-phosphatase-like, core domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
D-SERINE / Putative sulfatase
Similarity search - Component
Biological speciesMariniflexile fucanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsRoret, T. / Nikolic Chenais, J. / Poirot, Z. / Czjzek, M. / Michel, G.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE43-0003 France
CitationJournal: To Be Published
Title: X-ray structure of the S1_11 sulfatase MfFcsGS1_11 from Mariniflexile fucanivorans
Authors: Roret, T. / Nikolic Chenais, J. / Poirot, Z. / Czjzek, M. / Michel, G.
History
DepositionJul 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 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: Putative sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,14311
Polymers65,2341
Non-polymers91010
Water12,629701
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-88 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.196, 91.048, 109.363
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative sulfatase


Mass: 65233.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: suroxidized cysteine 84 / Source: (gene. exp.) Mariniflexile fucanivorans (bacteria) / Gene: EV196_102472 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4R1RP02

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Non-polymers , 5 types, 711 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 3,350 100 mM Ammonium sulfate 2 mM Calcium chloride 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.37→46.88 Å / Num. obs: 125387 / % possible obs: 99.2 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 27.1
Reflection shellResolution: 1.37→1.44 Å / Num. unique obs: 17898 / CC1/2: 0.903

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→45.52 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.687 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1692 6199 4.95 %
Rwork0.1449 118953 -
obs0.1461 125152 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.12 Å2
Refinement stepCycle: LAST / Resolution: 1.37→45.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 49 701 5113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084615
X-RAY DIFFRACTIONf_angle_d0.96326265
X-RAY DIFFRACTIONf_chiral_restr0.0802649
X-RAY DIFFRACTIONf_plane_restr0.0068812
X-RAY DIFFRACTIONf_dihedral_angle_d16.31491717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.39922130.31563832X-RAY DIFFRACTION97.52
1.39-1.40.31331970.2913903X-RAY DIFFRACTION97.6
1.4-1.420.29562100.27863846X-RAY DIFFRACTION97.55
1.42-1.440.30911920.27613899X-RAY DIFFRACTION97.73
1.44-1.460.27521910.28573895X-RAY DIFFRACTION97.68
1.46-1.480.30742030.25873856X-RAY DIFFRACTION97.88
1.48-1.50.35592000.24463911X-RAY DIFFRACTION97.83
1.5-1.520.28442160.23633853X-RAY DIFFRACTION97.84
1.52-1.540.22722060.22163929X-RAY DIFFRACTION98.27
1.54-1.570.27152040.20473849X-RAY DIFFRACTION98.11
1.57-1.60.24681960.1963925X-RAY DIFFRACTION98.26
1.6-1.620.21812330.18133933X-RAY DIFFRACTION98.58
1.62-1.660.21071890.15783928X-RAY DIFFRACTION98.63
1.66-1.690.18652170.13933923X-RAY DIFFRACTION99
1.69-1.730.19912050.13113964X-RAY DIFFRACTION99.12
1.73-1.770.18092130.12283936X-RAY DIFFRACTION98.93
1.77-1.810.15122120.11863964X-RAY DIFFRACTION99.38
1.81-1.860.14312270.11673947X-RAY DIFFRACTION99.24
1.86-1.910.15841860.12133999X-RAY DIFFRACTION99.5
1.91-1.980.15391860.12564002X-RAY DIFFRACTION99.52
1.98-2.050.15311780.13254012X-RAY DIFFRACTION99.57
2.05-2.130.17742190.13953995X-RAY DIFFRACTION99.76
2.13-2.230.162150.1314037X-RAY DIFFRACTION99.84
2.23-2.340.13762230.1213981X-RAY DIFFRACTION99.79
2.34-2.490.14332140.13024041X-RAY DIFFRACTION99.98
2.49-2.680.15481930.13324052X-RAY DIFFRACTION99.93
2.68-2.950.13962150.13484073X-RAY DIFFRACTION100
2.95-3.380.15432250.13344071X-RAY DIFFRACTION99.95
3.38-4.260.14352160.12554114X-RAY DIFFRACTION99.95
4.26-45.520.17172050.16074283X-RAY DIFFRACTION98.96

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