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- PDB-6ust: Gut microbial sulfatase from Hungatella hathewayi -

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Basic information

Entry
Database: PDB / ID: 6ust
TitleGut microbial sulfatase from Hungatella hathewayi
ComponentsN-acetylgalactosamine 6-sulfate sulfatase
KeywordsHYDROLASE / microbiome / arylsulfatase
Function / homology
Function and homology information


arylsulfatase (type I) / arylsulfatase activity / metal ion binding
Similarity search - Function
: / Sulfatases signature 2. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
N-acetylgalactosamine 6-sulfate sulfatase
Similarity search - Component
Biological speciesHungatella hathewayi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsErvin, S.M. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA22469 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Insights into Endobiotic Reactivation by Human Gut Microbiome-Encoded Sulfatases.
Authors: Ervin, S.M. / Simpson, J.B. / Gibbs, M.E. / Creekmore, B.C. / Lim, L. / Walton, W.G. / Gharaibeh, R.Z. / Redinbo, M.R.
History
DepositionOct 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylgalactosamine 6-sulfate sulfatase
B: N-acetylgalactosamine 6-sulfate sulfatase
C: N-acetylgalactosamine 6-sulfate sulfatase
D: N-acetylgalactosamine 6-sulfate sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,4258
Polymers211,2644
Non-polymers1604
Water4,864270
1
A: N-acetylgalactosamine 6-sulfate sulfatase
hetero molecules

D: N-acetylgalactosamine 6-sulfate sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7124
Polymers105,6322
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area3500 Å2
ΔGint-7 kcal/mol
Surface area31770 Å2
MethodPISA
2
B: N-acetylgalactosamine 6-sulfate sulfatase
hetero molecules

C: N-acetylgalactosamine 6-sulfate sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7124
Polymers105,6322
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3440 Å2
ΔGint-10 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.911, 114.668, 188.654
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
N-acetylgalactosamine 6-sulfate sulfatase


Mass: 52816.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungatella hathewayi (bacteria) / Gene: atsA, ERS852407_02004 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174CV66, arylsulfatase (type I)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL protein 0.2 M Potassium fluoride 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.59→23.7 Å / Num. obs: 60399 / % possible obs: 92.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 38.63 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.91
Reflection shellResolution: 2.5963→2.6611 Å / Num. unique obs: 5721 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BIA

6bia


Resolution: 2.6→23.7 Å / SU ML: 0.2937 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.1642
RfactorNum. reflection% reflection
Rfree0.2289 1986 3.29 %
Rwork0.1591 --
obs0.1614 60399 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.71 Å2
Refinement stepCycle: LAST / Resolution: 2.6→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14669 0 4 270 14943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007815104
X-RAY DIFFRACTIONf_angle_d0.924620519
X-RAY DIFFRACTIONf_chiral_restr0.05522080
X-RAY DIFFRACTIONf_plane_restr0.00612733
X-RAY DIFFRACTIONf_dihedral_angle_d4.97638868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.27281310.19743886X-RAY DIFFRACTION89.71
2.66-2.730.30211400.19634108X-RAY DIFFRACTION94.78
2.73-2.810.26211380.19434107X-RAY DIFFRACTION95.18
2.81-2.90.28271400.19194088X-RAY DIFFRACTION93.83
2.9-3.010.27341430.18744191X-RAY DIFFRACTION96.68
3.01-3.130.26411420.18354183X-RAY DIFFRACTION96.03
3.13-3.270.25521440.17484224X-RAY DIFFRACTION97.07
3.27-3.440.2331430.17024228X-RAY DIFFRACTION96.58
3.44-3.660.25511430.15754202X-RAY DIFFRACTION96.17
3.66-3.940.21381450.14814227X-RAY DIFFRACTION96.02
3.94-4.330.18751420.13824176X-RAY DIFFRACTION95.36
4.33-4.950.21121440.12434226X-RAY DIFFRACTION95
4.95-6.220.20391450.15114246X-RAY DIFFRACTION95.29
6.22-23.70.18951460.15244321X-RAY DIFFRACTION92.89

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