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- PDB-7snj: Structure of Bacple_01701, a 6-O-galactose porphyran sulfatase -

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Basic information

Entry
Database: PDB / ID: 7snj
TitleStructure of Bacple_01701, 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 / 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
CITRIC ACID / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / Arylsulfatase
Similarity search - Component
Biological speciesPhocaeicola plebeius DSM 17135 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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)63,61510
Polymers62,6451
Non-polymers9709
Water3,531196
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)154.860, 154.860, 46.320
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-805-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 62645.383 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

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Non-polymers , 7 types, 205 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#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


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 40% Peg 200, 100mM Sodium Citrate pH5.5, 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: 1.03 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 77429 / % possible obs: 99.9 % / Redundancy: 18.7 % / CC1/2: 1 / Net I/σ(I): 17.8
Reflection shellResolution: 1.74→1.86 Å / Num. unique obs: 11789 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G2V

5g2v


Resolution: 1.74→44.7 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 3271 5 %
Rwork0.1875 --
obs0.189 65435 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 64 196 4394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074305
X-RAY DIFFRACTIONf_angle_d0.8975799
X-RAY DIFFRACTIONf_dihedral_angle_d11.821593
X-RAY DIFFRACTIONf_chiral_restr0.054588
X-RAY DIFFRACTIONf_plane_restr0.008745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.770.65751410.61332674X-RAY DIFFRACTION100
1.77-1.790.49451410.5732689X-RAY DIFFRACTION100
1.79-1.820.47451410.47912667X-RAY DIFFRACTION100
1.82-1.850.41051410.42082687X-RAY DIFFRACTION100
1.85-1.890.37871410.36792675X-RAY DIFFRACTION100
1.89-1.920.33831420.31952697X-RAY DIFFRACTION100
1.92-1.960.32921400.27332669X-RAY DIFFRACTION100
1.96-2.010.25061410.26332674X-RAY DIFFRACTION100
2.01-2.050.28751410.24542668X-RAY DIFFRACTION100
2.05-2.10.24731430.2512717X-RAY DIFFRACTION100
2.1-2.160.2541390.23422673X-RAY DIFFRACTION100
2.16-2.220.23731420.20092690X-RAY DIFFRACTION100
2.22-2.30.23221420.18192689X-RAY DIFFRACTION100
2.3-2.380.20181420.16892702X-RAY DIFFRACTION100
2.38-2.470.23411410.16362689X-RAY DIFFRACTION100
2.47-2.590.22471430.16872715X-RAY DIFFRACTION100
2.59-2.720.21571440.17752719X-RAY DIFFRACTION100
2.72-2.890.19861420.18042704X-RAY DIFFRACTION100
2.89-3.120.21321430.17512714X-RAY DIFFRACTION100
3.12-3.430.21381420.17092708X-RAY DIFFRACTION100
3.43-3.930.17291450.15232755X-RAY DIFFRACTION100
3.93-4.950.1811450.13492744X-RAY DIFFRACTION100
4.95-44.70.19261490.1812845X-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)
12.0007-0.48520.05881.8928-0.12820.5906-0.06850.0232-0.11450.03540.0227-0.164-0.00520.09350.04850.4247-0.08380.01940.3816-0.0040.351835.804941.10811.1354
21.3252-0.94630.11065.5669-0.04950.6026-0.0377-0.0781-0.06090.71060.013-0.2193-0.26620.21190.00850.5402-0.1222-0.10030.46430.0450.476646.619751.281621.2933
32.6022-0.19310.19571.86220.13450.5152-0.16850.10530.14920.04080.0330.0121-0.13640.05770.13370.5275-0.10730.01790.41730.02580.363330.129253.7910.9985
41.5032-0.2624-0.12281.06150.13610.5467-0.0937-0.0139-0.06720.11280.00520.0877-0.02080.04640.08420.4365-0.06120.03930.36110.00020.360925.548942.165813.0063
52.0597-1.00961.05462.424-0.97082.143-0.03890.1199-0.5360.046-0.03460.3320.2542-0.06640.00930.4684-0.08410.1230.3835-0.04310.633916.043425.376412.8186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 246 )
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 482 )
5X-RAY DIFFRACTION5chain 'A' and (resid 483 through 536 )

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