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- PDB-9bba: Structure of S1_8C, a lambda-carrageenan specific sulfatase -

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Basic information

Entry
Database: PDB / ID: 9bba
TitleStructure of S1_8C, a lambda-carrageenan specific sulfatase
ComponentsS1_8C sulfatase
KeywordsSUGAR BINDING PROTEIN / Sulfatase / carrageenan
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.201 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_8C sulfatase
B: S1_8C sulfatase
C: S1_8C sulfatase
D: S1_8C sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,94112
Polymers299,6124
Non-polymers3298
Water8,197455
1
A: S1_8C sulfatase
B: S1_8C sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0558
Polymers149,8062
Non-polymers2496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: S1_8C sulfatase
D: S1_8C sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,8864
Polymers149,8062
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.897, 54.565, 159.287
Angle α, β, γ (deg.)90.00, 113.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
S1_8C sulfatase


Mass: 74903.094 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350, 0.15 M sodium nitrate, 5% glycerol

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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: 2.2→30 Å / Num. obs: 123433 / % possible obs: 98 % / Redundancy: 4.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.043 / Net I/σ(I): 13.5
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5100 / CC1/2: 0.824 / Rpim(I) all: 0.231

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→29.155 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 6038 4.92 %
Rwork0.1874 --
obs0.1899 122669 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→29.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19119 0 11 455 19585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819645
X-RAY DIFFRACTIONf_angle_d1.126658
X-RAY DIFFRACTIONf_dihedral_angle_d12.4957168
X-RAY DIFFRACTIONf_chiral_restr0.0432871
X-RAY DIFFRACTIONf_plane_restr0.0053475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.22570.30931640.22153262X-RAY DIFFRACTION83
2.2257-2.25190.2841680.21633673X-RAY DIFFRACTION91
2.2519-2.27940.27271710.22053735X-RAY DIFFRACTION93
2.2794-2.30820.29281770.21173687X-RAY DIFFRACTION93
2.3082-2.33860.27731810.20783737X-RAY DIFFRACTION94
2.3386-2.37060.27611780.21753833X-RAY DIFFRACTION94
2.3706-2.40440.30152190.22193725X-RAY DIFFRACTION95
2.4044-2.44030.29882030.22763791X-RAY DIFFRACTION96
2.4403-2.47840.34142160.22393875X-RAY DIFFRACTION97
2.4784-2.5190.28611890.22093773X-RAY DIFFRACTION97
2.519-2.56240.30412040.22043864X-RAY DIFFRACTION98
2.5624-2.6090.26792130.22593943X-RAY DIFFRACTION98
2.609-2.65920.27622180.21423899X-RAY DIFFRACTION99
2.6592-2.71340.28692090.21323960X-RAY DIFFRACTION99
2.7134-2.77230.29832270.21783895X-RAY DIFFRACTION99
2.7723-2.83680.28292000.22033990X-RAY DIFFRACTION99
2.8368-2.90770.27831960.23063933X-RAY DIFFRACTION99
2.9077-2.98620.27722010.22463921X-RAY DIFFRACTION98
2.9862-3.0740.3092010.22553974X-RAY DIFFRACTION99
3.074-3.17310.26082400.22173879X-RAY DIFFRACTION99
3.1731-3.28640.27322150.22533954X-RAY DIFFRACTION99
3.2864-3.41770.2681870.20454040X-RAY DIFFRACTION99
3.4177-3.5730.2231880.19133997X-RAY DIFFRACTION100
3.573-3.7610.21541890.17114012X-RAY DIFFRACTION100
3.761-3.99610.21322210.16193964X-RAY DIFFRACTION99
3.9961-4.30380.18222250.14863993X-RAY DIFFRACTION99
4.3038-4.73520.1671860.13174026X-RAY DIFFRACTION99
4.7352-5.41660.19162130.14364060X-RAY DIFFRACTION99
5.4166-6.810.21951960.16474096X-RAY DIFFRACTION100
6.81-29.1550.16252430.15134140X-RAY DIFFRACTION99

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