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- PDB-8di0: Bfo2290: Tannerella forsythia chondroitin sulfate A sulfatase -

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Basic information

Entry
Database: PDB / ID: 8di0
TitleBfo2290: Tannerella forsythia chondroitin sulfate A sulfatase
ComponentsArylsulfatase
KeywordsLYASE / Carbohydrate sulfatase / sulfatase / chondroitin sulfate A
Function / homologyHydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Arylsulfatase
Function and homology information
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSuits, M.D.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)DDG-2020-00007 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-05018 Canada
CitationJournal: Plos One / Year: 2022
Title: Degradation of chondroitin sulfate A by a PUL-like operon in Tannerella forsythia.
Authors: Nguyen, P. / Eshaque, R. / Garland, B.A. / Dang, A. / Suits, M.D.L.
History
DepositionJun 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Arylsulfatase
B: Arylsulfatase
C: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,2654
Polymers178,1693
Non-polymers961
Water34219
1
A: Arylsulfatase


Theoretical massNumber of molelcules
Total (without water)59,3901
Polymers59,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arylsulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4862
Polymers59,3901
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arylsulfatase


Theoretical massNumber of molelcules
Total (without water)59,3901
Polymers59,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.180, 121.110, 144.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Arylsulfatase


Mass: 59389.664 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (strain ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338) (bacteria)
Strain: ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338
Gene: BFO_2290 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: G8UJW8, Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.6
Details: 100 mM sodium citrate pH 5.6, 0.5 M ammonium sulfate, and 1 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98011 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.85→48.32 Å / Num. obs: 47086 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 69.03 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.057 / Net I/σ(I): 12.5
Reflection shellResolution: 2.85→3 Å / Num. unique obs: 6774 / CC1/2: 0.599 / Rpim(I) all: 0.528

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J66

6j66


Resolution: 2.85→48.32 Å / SU ML: 0.4381 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2805 2355 5 %
Rwork0.2223 44724 -
obs0.2251 47079 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.88 Å2
Refinement stepCycle: LAST / Resolution: 2.85→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10749 0 5 19 10773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003411049
X-RAY DIFFRACTIONf_angle_d0.718714996
X-RAY DIFFRACTIONf_chiral_restr0.04481579
X-RAY DIFFRACTIONf_plane_restr0.00811962
X-RAY DIFFRACTIONf_dihedral_angle_d5.7581465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.910.36391370.29862598X-RAY DIFFRACTION100
2.91-2.970.3811360.30872580X-RAY DIFFRACTION99.96
2.97-3.040.42841360.31912585X-RAY DIFFRACTION100
3.04-3.120.37311360.30952596X-RAY DIFFRACTION99.96
3.12-3.20.31511390.26922624X-RAY DIFFRACTION99.96
3.2-3.290.31541350.25512582X-RAY DIFFRACTION100
3.3-3.40.35071380.24572609X-RAY DIFFRACTION100
3.4-3.520.32731370.23372611X-RAY DIFFRACTION100
3.52-3.660.31651380.24222621X-RAY DIFFRACTION99.96
3.66-3.830.27491380.22882612X-RAY DIFFRACTION100
3.83-4.030.25241380.19372620X-RAY DIFFRACTION99.96
4.03-4.280.24411380.18642629X-RAY DIFFRACTION100
4.28-4.620.25341380.18142629X-RAY DIFFRACTION100
4.62-5.080.23161400.18162651X-RAY DIFFRACTION99.96
5.08-5.810.24541400.20372667X-RAY DIFFRACTION100
5.81-7.320.26931420.24352695X-RAY DIFFRACTION100
7.32-48.320.27061490.21482815X-RAY DIFFRACTION99.8

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