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- PDB-9bas: Structure of S1_15A, a lambda-carrageenan specific sulfatase, in ... -

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Basic information

Entry
Database: PDB / ID: 9bas
TitleStructure of S1_15A, a lambda-carrageenan specific sulfatase, in complex with galactose-6-sulfate
ComponentsS1_15A sulfatase
KeywordsSUGAR BINDING PROTEIN / Sulfatase / carrageenan
Function / homology6-O-sulfo-beta-D-galactopyranose
Function and homology information
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.791 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_15A, a lambda-carrageenan specific sulfatase, in complex with galactose-6-sulfate
Authors: Hettle, J.A. / Vickers, C. / Boraston, A.B.
History
DepositionApr 4, 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
B: S1_15A sulfatase
A: S1_15A sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2026
Polymers115,6022
Non-polymers6014
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.866, 110.007, 71.791
Angle α, β, γ (deg.)90.00, 106.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein S1_15A sulfatase


Mass: 57800.926 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)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-G6S / 6-O-sulfo-beta-D-galactopyranose / D-GALACTOSE-6-SULFATE / 6-O-sulfo-beta-D-galactose / 6-O-sulfo-D-galactose / 6-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 260.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalp[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
6-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-Galp6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 23.5% PEG 3350, 5% glycerol, 3% ethylene glycol, 0.2 M ammonium citrate dibasic (pH 5.0)

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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 20, 2020 / Details: VariMaxTM-HF ArcSec Confocal Optical System
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→30 Å / Num. obs: 99922 / % possible obs: 99.8 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.032 / Net I/σ(I): 19.1
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.368 / Num. unique obs: 3713 / CC1/2: 0.892 / Rpim(I) all: 0.198

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.791→29.541 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.27 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.236 4944 5.06 %
Rwork0.1869 --
obs0.1907 97657 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.791→29.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7423 0 34 219 7676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087662
X-RAY DIFFRACTIONf_angle_d1.17710401
X-RAY DIFFRACTIONf_dihedral_angle_d14.3782820
X-RAY DIFFRACTIONf_chiral_restr0.0441123
X-RAY DIFFRACTIONf_plane_restr0.0061362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7928-1.82370.28912150.25333713X-RAY DIFFRACTION75
1.8237-1.85680.3322080.24814102X-RAY DIFFRACTION83
1.8568-1.89250.27512280.2334396X-RAY DIFFRACTION87
1.8925-1.93110.30762220.23224529X-RAY DIFFRACTION91
1.9311-1.9730.24262400.21744657X-RAY DIFFRACTION94
1.973-2.01890.27512920.20554682X-RAY DIFFRACTION94
2.0189-2.06930.2822320.20444719X-RAY DIFFRACTION95
2.0693-2.12520.24741940.20364823X-RAY DIFFRACTION96
2.1252-2.18770.26872670.20444708X-RAY DIFFRACTION95
2.1877-2.25820.25022590.20054728X-RAY DIFFRACTION95
2.2582-2.33880.2592360.20214772X-RAY DIFFRACTION95
2.3388-2.43220.28982150.19914742X-RAY DIFFRACTION96
2.4322-2.54270.23462750.20054724X-RAY DIFFRACTION94
2.5427-2.67650.27782480.19734789X-RAY DIFFRACTION95
2.6765-2.84370.23782310.20344729X-RAY DIFFRACTION95
2.8437-3.06250.24642460.20084774X-RAY DIFFRACTION95
3.0625-3.36930.24482890.18764713X-RAY DIFFRACTION94
3.3693-3.85360.20052410.16574775X-RAY DIFFRACTION95
3.8536-4.8430.17092600.14344795X-RAY DIFFRACTION95
4.843-19.59720.20162800.16024801X-RAY DIFFRACTION94

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