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

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Basic information

Entry
Database: PDB / ID: 9bav
TitleStructure of S1_15B, a lambda-carrageenan specific sulfatase, in complex with a carrageenoligosaccharide
ComponentsS1_15B sulfatase
KeywordsSUGAR BINDING PROTEIN / Sulfatase / carrageenan
Function / homology: / 6-O-sulfo-beta-D-galactopyranose
Function and homology information
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.494 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 a carrageenoligosaccharide
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)117,39413
Polymers115,6422
Non-polymers1,75211
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.229, 92.870, 176.478
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_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)

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Sugars , 3 types, 3 molecules

#2: Polysaccharide 6-O-sulfo-alpha-D-galactopyranose-(1-3)-2-O-sulfo-beta-D-galactopyranose-(1-4)-2,6-di-O-sulfo-alpha- ...6-O-sulfo-alpha-D-galactopyranose-(1-3)-2-O-sulfo-beta-D-galactopyranose-(1-4)-2,6-di-O-sulfo-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 824.690 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
[][a-D-Galp2SO36SO3]{[(4+1)][b-D-Galp2SO3]{[(3+1)][a-D-Galp6SO3]{}}}LINUCSPDB-CARE
#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.: 1 / 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
#7: Sugar ChemComp-A1APC / 6-O-sulfo-alpha-D-galactopyranose


Type: D-saccharide, alpha linking / Mass: 260.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O9S / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 99 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.2 M ammonium sulfate, 3% 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: 2.49→30 Å / Num. obs: 38235 / % possible obs: 98.8 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Net I/σ(I): 19.1
Reflection shellResolution: 2.49→2.54 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2465 / CC1/2: 0.953 / Rpim(I) all: 0.154

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.494→29.532 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 1884 4.99 %
Rwork0.2003 --
obs0.2036 37768 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.494→29.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7539 0 100 91 7730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097811
X-RAY DIFFRACTIONf_angle_d1.25910632
X-RAY DIFFRACTIONf_dihedral_angle_d4.2224631
X-RAY DIFFRACTIONf_chiral_restr0.0651185
X-RAY DIFFRACTIONf_plane_restr0.0092342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4941-2.56150.39851280.26652465X-RAY DIFFRACTION88
2.5615-2.63680.38171410.25072678X-RAY DIFFRACTION96
2.6368-2.72190.31711470.25782713X-RAY DIFFRACTION97
2.7219-2.81910.34721370.26322739X-RAY DIFFRACTION98
2.8191-2.93190.35721490.24892755X-RAY DIFFRACTION99
2.9319-3.06520.31181640.24022768X-RAY DIFFRACTION99
3.0652-3.22660.28741320.22712797X-RAY DIFFRACTION99
3.2266-3.42840.32091410.23032762X-RAY DIFFRACTION98
3.4284-3.69270.26081390.20422779X-RAY DIFFRACTION98
3.6927-4.06350.22421470.17022758X-RAY DIFFRACTION98
4.0635-4.64950.21661460.14952830X-RAY DIFFRACTION99
4.6495-5.85040.21161610.16262849X-RAY DIFFRACTION99
5.8504-29.5320.21481520.17662991X-RAY DIFFRACTION99

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