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- PDB-9bes: Structure of S1_8A, a lambda-carrageenan specific sulfatase, in c... -

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Basic information

Entry
Database: PDB / ID: 9bes
TitleStructure of S1_8A, a lambda-carrageenan specific sulfatase, in complex with monosaccharide
Components(S1_8A Sulfatase) x 2
KeywordsSUGAR BINDING PROTEIN / Sulfatase / carrageenan
Function / homologybeta-D-galactopyranose
Function and homology information
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.079 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_8A, a lambda-carrageenan specific sulfatase, in complex with monosaccharide
Authors: Hettle, J.A. / Vickers, C. / Boraston, A.B.
History
DepositionApr 16, 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_8A Sulfatase
B: S1_8A Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,5706
Polymers119,2482
Non-polymers3224
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.683, 56.202, 97.232
Angle α, β, γ (deg.)77.44, 76.06, 64.03
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein S1_8A Sulfatase


Mass: 59510.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas distincta (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein S1_8A Sulfatase


Mass: 59737.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cys 82 was post-translationally modified to formylglycine, which reacted with the added monosaccharide
Source: (gene. exp.) Pseudoalteromonas distincta (bacteria) / Production host: Escherichia coli (E. coli)

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Sugars , 1 types, 1 molecules

#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 241 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.97 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 5% glycerol, 5% Jeffamine ED-2001 (pH 7.0), 0.1 M arginine, 0.1 M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.079→30 Å / Num. obs: 51285 / % possible obs: 95 % / Redundancy: 2.8 % / CC1/2: 0.981 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.069 / Net I/σ(I): 9.9
Reflection shellResolution: 2.079→2.14 Å / Rmerge(I) obs: 0.297 / Num. unique obs: 2331 / CC1/2: 0.915 / Rpim(I) all: 0.146

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.079→29.278 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 2546 5.09 %
Rwork0.1987 --
obs0.202 49981 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.079→29.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7703 0 18 238 7959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087942
X-RAY DIFFRACTIONf_angle_d1.17910794
X-RAY DIFFRACTIONf_dihedral_angle_d2.7046483
X-RAY DIFFRACTIONf_chiral_restr0.0551156
X-RAY DIFFRACTIONf_plane_restr0.0061402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.079-2.1190.3435740.23321522X-RAY DIFFRACTION53
2.119-2.16220.29651380.21052371X-RAY DIFFRACTION80
2.1622-2.20920.29571300.20272469X-RAY DIFFRACTION88
2.2092-2.26060.2451360.20642700X-RAY DIFFRACTION91
2.2606-2.31710.28751420.2022614X-RAY DIFFRACTION93
2.3171-2.37970.29691420.19812732X-RAY DIFFRACTION94
2.3797-2.44970.29891320.20612836X-RAY DIFFRACTION96
2.4497-2.52880.30221240.21542739X-RAY DIFFRACTION96
2.5288-2.61910.27261900.21852768X-RAY DIFFRACTION96
2.6191-2.72390.33051420.22812749X-RAY DIFFRACTION96
2.7239-2.84770.30971530.24272773X-RAY DIFFRACTION96
2.8477-2.99770.30811400.24912759X-RAY DIFFRACTION96
2.9977-3.18530.34351520.23962759X-RAY DIFFRACTION96
3.1853-3.43090.26811440.20492741X-RAY DIFFRACTION95
3.4309-3.77560.22371480.18522711X-RAY DIFFRACTION93
3.7756-4.32040.2171740.17212692X-RAY DIFFRACTION94
4.3204-5.43750.24641410.16122715X-RAY DIFFRACTION95
5.4375-29.2780.18991440.16662785X-RAY DIFFRACTION96

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