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- PDB-7oze: Sulfated host glycan recognition by carbohydrate sulfatases of th... -

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Basic information

Entry
Database: PDB / ID: 7oze
TitleSulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT1624-S1_15)
ComponentsPutative secreted sulfatase
KeywordsHYDROLASE / Host glycans / sulfation / carbohydrate sulfatases / microbiota
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
6-O-sulfo-beta-D-galactopyranose / Secreted sulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota.
Authors: Luis, A.S. / Basle, A. / Byrne, D.P. / Wright, G.S.A. / London, J.A. / Jin, C. / Karlsson, N.G. / Hansson, G.C. / Eyers, P.A. / Czjzek, M. / Barbeyron, T. / Yates, E.A. / Martens, E.C. / Cartmell, A.
History
DepositionJun 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Putative secreted sulfatase
EEE: Putative secreted sulfatase
FFF: Putative secreted sulfatase
GGG: Putative secreted sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,70212
Polymers224,5014
Non-polymers1,2018
Water4,810267
1
AAA: Putative secreted sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4253
Polymers56,1251
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
EEE: Putative secreted sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4253
Polymers56,1251
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
FFF: Putative secreted sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4253
Polymers56,1251
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
GGG: Putative secreted sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4253
Polymers56,1251
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.401, 124.715, 97.137
Angle α, β, γ (deg.)90.000, 95.321, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21EEE
32AAA
42FFF
53AAA
63GGG
74EEE
84FFF
95EEE
105GGG
116FFF
126GGG

NCS domain segments:

Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 29 - 515 / Label seq-ID: 27 - 513

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AAAA
221EEEB
332AAAA
442FFFC
553AAAA
663GGGD
774EEEB
884FFFC
995EEEB
10105GGGD
11116FFFC
12126GGGD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Putative secreted sulfatase


Mass: 56125.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_1624
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A7A1
#2: Sugar
ChemComp-G6S / 6-O-sulfo-beta-D-galactopyranose / D-GALACTOSE-6-SULFATE / 6-O-sulfo-beta-D-galactose / 6-O-sulfo-D-galactose / 6-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 260.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalp[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
6-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-Galp6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mg/ml BT1624-S1_15 with 10 mM 6S-GalNAc crystallised in 20 % PEG 6000, 0.2 M ammonium chloride and 0.1 M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50.54 Å / Num. obs: 56316 / % possible obs: 100 % / Redundancy: 3.7 % / CC1/2: 0.927 / Net I/σ(I): 3
Reflection shellResolution: 2.7→2.78 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4596 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S20

6s20


Resolution: 2.7→50.5 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.837 / SU B: 17.056 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / ESU R Free: 0.387
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2635 2741 4.877 %
Rwork0.2287 53456 -
all0.23 --
obs-56197 99.709 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.134 Å20 Å21.09 Å2
2--2.044 Å20 Å2
3----1.094 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14891 0 68 267 15226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01315361
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714188
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.64820894
X-RAY DIFFRACTIONr_angle_other_deg1.1381.58532703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77851950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43723.1771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.453152403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3961580
X-RAY DIFFRACTIONr_chiral_restr0.0510.21947
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023516
X-RAY DIFFRACTIONr_nbd_refined0.1850.22947
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.213469
X-RAY DIFFRACTIONr_nbtor_refined0.1540.27307
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.27164
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2452
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1990.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.234
X-RAY DIFFRACTIONr_nbd_other0.2220.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.24
X-RAY DIFFRACTIONr_mcbond_it0.7121.7777803
X-RAY DIFFRACTIONr_mcbond_other0.7121.7777802
X-RAY DIFFRACTIONr_mcangle_it1.2472.6649752
X-RAY DIFFRACTIONr_mcangle_other1.2472.6649753
X-RAY DIFFRACTIONr_scbond_it0.6471.8377558
X-RAY DIFFRACTIONr_scbond_other0.6471.8377558
X-RAY DIFFRACTIONr_scangle_it1.1472.72511142
X-RAY DIFFRACTIONr_scangle_other1.1462.72511143
X-RAY DIFFRACTIONr_lrange_it2.75620.25216684
X-RAY DIFFRACTIONr_lrange_other2.75420.25916674
X-RAY DIFFRACTIONr_ncsr_local_group_10.0450.0515832
X-RAY DIFFRACTIONr_ncsr_local_group_20.050.0515791
X-RAY DIFFRACTIONr_ncsr_local_group_30.0440.0515843
X-RAY DIFFRACTIONr_ncsr_local_group_40.0510.0515771
X-RAY DIFFRACTIONr_ncsr_local_group_50.0470.0515796
X-RAY DIFFRACTIONr_ncsr_local_group_60.0510.0515739
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.045140.0501
12EEEX-RAY DIFFRACTIONLocal ncs0.045140.0501
23AAAX-RAY DIFFRACTIONLocal ncs0.049620.0501
24FFFX-RAY DIFFRACTIONLocal ncs0.049620.0501
35AAAX-RAY DIFFRACTIONLocal ncs0.044090.0501
36GGGX-RAY DIFFRACTIONLocal ncs0.044090.0501
47EEEX-RAY DIFFRACTIONLocal ncs0.051460.0501
48FFFX-RAY DIFFRACTIONLocal ncs0.051460.0501
59EEEX-RAY DIFFRACTIONLocal ncs0.046670.0501
510GGGX-RAY DIFFRACTIONLocal ncs0.046670.0501
611FFFX-RAY DIFFRACTIONLocal ncs0.050760.0501
612GGGX-RAY DIFFRACTIONLocal ncs0.050760.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.3181990.2953918X-RAY DIFFRACTION99.3485
2.77-2.8460.3561720.2953839X-RAY DIFFRACTION99.6769
2.846-2.9280.3222000.2793745X-RAY DIFFRACTION99.7724
2.928-3.0180.2911830.2643619X-RAY DIFFRACTION99.6592
3.018-3.1170.2881590.2613536X-RAY DIFFRACTION99.8379
3.117-3.2270.3191700.2493422X-RAY DIFFRACTION99.8888
3.227-3.3480.2421790.2463289X-RAY DIFFRACTION99.9712
3.348-3.4850.311630.2433147X-RAY DIFFRACTION99.8492
3.485-3.640.2721580.2293014X-RAY DIFFRACTION100
3.64-3.8170.2531530.2052909X-RAY DIFFRACTION99.9021
3.817-4.0240.2311330.1942780X-RAY DIFFRACTION99.8971
4.024-4.2670.1891310.1812633X-RAY DIFFRACTION99.8194
4.267-4.5620.2121490.1742436X-RAY DIFFRACTION99.8455
4.562-4.9270.2161160.1752279X-RAY DIFFRACTION99.8333
4.927-5.3960.246940.1932149X-RAY DIFFRACTION99.6446
5.396-6.0310.2441090.2331885X-RAY DIFFRACTION99.6502
6.031-6.9620.316900.2471689X-RAY DIFFRACTION99.6639
6.962-8.520.255760.1931435X-RAY DIFFRACTION99.4733
8.52-12.0210.188660.1991114X-RAY DIFFRACTION99.7464
12.021-50.50.208410.29618X-RAY DIFFRACTION98.2116

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