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- PDB-7sno: Structure of Bacple_01701(H214N), a 6-O-galactose porphyran sulfatase -

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Basic information

Entry
Database: PDB / ID: 7sno
TitleStructure of Bacple_01701(H214N), a 6-O-galactose porphyran sulfatase
ComponentsArylsulfatase
KeywordsHYDROLASE / 6-O-galactose porphyran sulfatase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / sulfuric ester hydrolase activity
Similarity search - Function
N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Arylsulfatase
Similarity search - Component
Biological speciesPhocaeicola plebeius DSM 17135 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUlaganathan, T. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biorxiv / Year: 2023
Title: The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations
Authors: Mathieu, S. / Touvrey, M. / Poulet, L. / Drouillard, S. / Ulaganathan, T.S. / Segurel, L. / Cygler, M. / Helbert, W.
History
DepositionOct 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,27611
Polymers62,6211
Non-polymers1,65510
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.720, 154.720, 45.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-859-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Arylsulfatase / / 6-O-galactose porphyran sulfatase


Mass: 62621.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola plebeius DSM 17135 (bacteria)
Gene: BACPLE_01701
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B5CYA4, Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases
#2: Polysaccharide 6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-6-O-sulfo-alpha-L- ...6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-6-O-sulfo-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 826.704 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LGalp[6S]a1-3DGalpb1-4LGalp[6S]a1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2112h-1b_1-5][a1221h-1a_1-5_6*OSO/3=O/3=O]/1-2-1-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-L-Galp6SO3]{[(4+1)][b-D-Galp]{[(3+1)][a-L-Galp6SO3]{}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 237 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40% PEG 400, 100mM Sodium Citrate pH 5.5, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 37128 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.99 / Net I/σ(I): 10.24
Reflection shellResolution: 2.1→2.22 Å / Mean I/σ(I) obs: 1.38 / Num. unique obs: 57365 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
XDSdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SNJ

7snj


Resolution: 2.1→44.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2159 1853 5 %
Rwork0.1812 --
obs0.183 37092 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 107 228 4468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094344
X-RAY DIFFRACTIONf_angle_d1.0365860
X-RAY DIFFRACTIONf_dihedral_angle_d13.207620
X-RAY DIFFRACTIONf_chiral_restr0.059609
X-RAY DIFFRACTIONf_plane_restr0.009747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.36721410.31632673X-RAY DIFFRACTION100
2.16-2.220.31921410.30592671X-RAY DIFFRACTION100
2.22-2.290.32551420.26352702X-RAY DIFFRACTION100
2.29-2.370.27131410.23882680X-RAY DIFFRACTION100
2.37-2.470.27551410.21652692X-RAY DIFFRACTION100
2.47-2.580.25441420.20772690X-RAY DIFFRACTION100
2.58-2.720.22441430.19562715X-RAY DIFFRACTION100
2.72-2.890.24751420.19472691X-RAY DIFFRACTION100
2.89-3.110.2321420.18032712X-RAY DIFFRACTION100
3.11-3.420.20841420.17152707X-RAY DIFFRACTION100
3.42-3.920.22611440.14832725X-RAY DIFFRACTION100
3.92-4.940.14261440.13262751X-RAY DIFFRACTION100
4.94-44.660.18231480.17062830X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5781-0.28820.15421.3546-0.29161.0306-0.0447-0.0756-0.26420.0725-0.0104-0.16370.03020.12830.0580.2818-0.03-0.00690.25810.00510.458437.471641.394911.946
21.8543-2.5211-0.62294.3007-0.22422.4085-0.1293-0.1359-0.16930.7222-0.1027-0.0055-0.03580.19030.18840.4206-0.0737-0.1120.33550.03310.629146.036850.895725.6285
30.8087-1.52310.42144.35030.00911.12370.0478-0.1468-0.0160.0613-0.020.0454-0.10640.0587-0.03960.3629-0.101-0.01470.3210.02750.527642.132556.520113.3877
41.2712-0.2623-0.2310.82790.0470.4668-0.02850.04460.0230.0259-0.00630.0476-0.03090.02050.02080.273-0.0302-0.00730.2463-0.00140.410626.752144.64919.907
51.25840.03310.28110.67730.35912.4729-0.0529-0.0423-0.28270.0498-0.04240.21430.3009-0.06930.10660.3032-0.0450.06250.2446-0.00820.547916.715331.011618.2715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 433 )
5X-RAY DIFFRACTION5chain 'A' and (resid 434 through 542 )

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