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- PDB-9bau: Structure of S1_15B, a lambda-carrageenan specific sulfatase, in ... -

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Basic information

Entry
Database: PDB / ID: 9bau
TitleStructure of S1_15B, a lambda-carrageenan specific sulfatase, in complex with galactose-6-sulfate
ComponentsS1_15B 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: 2.301 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_15B, 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
A: S1_15B sulfatase
B: S1_15B sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,42011
Polymers115,6422
Non-polymers7789
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-71 kcal/mol
Surface area33420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.744, 93.847, 176.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein S1_15B sulfatase


Mass: 57820.961 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.2 M ammonium sulfate, 2% glycerol, 0.1 M arginine, 0.1 M Tris:HCl (pH 8.5)

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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 20, 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: 49811 / % possible obs: 99.7 % / Redundancy: 4.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.047 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.385 / Num. unique obs: 2410 / CC1/2: 0.785 / Rpim(I) all: 0.254

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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: 2.301→29.615 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 2460 4.98 %
Rwork0.1876 --
obs0.1902 49437 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→29.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7525 0 39 203 7767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087744
X-RAY DIFFRACTIONf_angle_d0.9610540
X-RAY DIFFRACTIONf_dihedral_angle_d3.7735491
X-RAY DIFFRACTIONf_chiral_restr0.0581173
X-RAY DIFFRACTIONf_plane_restr0.0061376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.3450.26761230.22152410X-RAY DIFFRACTION94
2.345-2.39280.28941290.21682530X-RAY DIFFRACTION97
2.3928-2.44480.29081330.222521X-RAY DIFFRACTION98
2.4448-2.50170.27161210.22062598X-RAY DIFFRACTION98
2.5017-2.56420.27071120.20952605X-RAY DIFFRACTION99
2.5642-2.63350.27221270.21542596X-RAY DIFFRACTION100
2.6335-2.71090.25241310.20822608X-RAY DIFFRACTION100
2.7109-2.79840.27671470.21112612X-RAY DIFFRACTION100
2.7984-2.89830.26261460.21132612X-RAY DIFFRACTION100
2.8983-3.01420.26811530.21832586X-RAY DIFFRACTION100
3.0142-3.15130.29021260.21842627X-RAY DIFFRACTION100
3.1513-3.31720.28931420.20732625X-RAY DIFFRACTION100
3.3172-3.52470.26891610.19942598X-RAY DIFFRACTION99
3.5247-3.79640.21861370.17282633X-RAY DIFFRACTION100
3.7964-4.17750.19771420.16232626X-RAY DIFFRACTION98
4.1775-4.77980.19631360.14362666X-RAY DIFFRACTION99
4.7798-6.01370.1971410.16692699X-RAY DIFFRACTION100
6.0137-29.6150.21251530.17172825X-RAY DIFFRACTION100

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