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- PDB-9bbd: Structure of S1_8B, a lambda-carrageenan specific sulfatase -

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Basic information

Entry
Database: PDB / ID: 9bbd
TitleStructure of S1_8B, a lambda-carrageenan specific sulfatase
ComponentsS1_8B sulfatase
KeywordsSUGAR BINDING PROTEIN / Sulfatase / carrageenan
Function / homologyACETATE ION
Function and homology information
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHettle, J.A. / Vickers, C. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: Structure of S1_8C, a lambda-carrageenan specific sulfatase
Authors: Hettle, J.A. / Vickers, C. / Boraston, A.B.
History
DepositionApr 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S1_8B sulfatase
B: S1_8B sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,58625
Polymers124,1232
Non-polymers1,46323
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-176 kcal/mol
Surface area36660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.842, 103.087, 148.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein S1_8B sulfatase


Mass: 62061.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas distincta (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 379 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2M ammonium sulfate, 0.1M sodium acetate (pH 4.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 425774 / % possible obs: 96.1 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.5
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.436 / Num. unique obs: 2000 / CC1/2: 0.869

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.933 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 3107 5.11 %
Rwork0.2028 --
obs0.2044 60746 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7310 0 73 356 7739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087579
X-RAY DIFFRACTIONf_angle_d0.89810310
X-RAY DIFFRACTIONf_dihedral_angle_d6.1775314
X-RAY DIFFRACTIONf_chiral_restr0.0521072
X-RAY DIFFRACTIONf_plane_restr0.0061340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33310.3099940.2641571X-RAY DIFFRACTION57
2.3331-2.37130.30241090.2391925X-RAY DIFFRACTION70
2.3713-2.41220.26721130.23992125X-RAY DIFFRACTION77
2.4122-2.45610.33161460.24142276X-RAY DIFFRACTION84
2.4561-2.50330.30571270.25292514X-RAY DIFFRACTION91
2.5033-2.55440.34141640.25532625X-RAY DIFFRACTION96
2.5544-2.60990.28581440.24872759X-RAY DIFFRACTION100
2.6099-2.67050.281500.23722727X-RAY DIFFRACTION100
2.6705-2.73730.31921450.24712769X-RAY DIFFRACTION99
2.7373-2.81120.3071480.25092720X-RAY DIFFRACTION99
2.8112-2.89390.26291620.25522721X-RAY DIFFRACTION99
2.8939-2.98720.31711240.25412761X-RAY DIFFRACTION99
2.9872-3.09390.34341340.24752763X-RAY DIFFRACTION99
3.0939-3.21760.25981260.2322814X-RAY DIFFRACTION99
3.2176-3.36390.27621290.22362787X-RAY DIFFRACTION100
3.3639-3.5410.22171510.19332789X-RAY DIFFRACTION100
3.541-3.76240.19321410.17492825X-RAY DIFFRACTION100
3.7624-4.05230.17291590.17052753X-RAY DIFFRACTION99
4.0523-4.45890.18751400.14992793X-RAY DIFFRACTION98
4.4589-5.10130.18731510.15712813X-RAY DIFFRACTION99
5.1013-6.41670.2231710.18092836X-RAY DIFFRACTION100
6.4167-29.9330.18281790.19092973X-RAY DIFFRACTION100

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