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- PDB-6ptk: Crystal structure of the sulfatase PsS1_NC C84A with bound sulfate ion -

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Basic information

Entry
Database: PDB / ID: 6ptk
TitleCrystal structure of the sulfatase PsS1_NC C84A with bound sulfate ion
Componentsexo-2S-iota carrageenan S1 sulfatase
KeywordsHYDROLASE / S1 sulfatase
Function / homologySulfatases signature 1. / Sulfatase, conserved site / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / 3,6-anhydro-D-galactose / 4-O-sulfo-beta-D-galactopyranose / Sulfatase
Function and homology information
Biological speciesPseudoalteromonas fuliginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHettle, A.G. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Commun Biol / Year: 2019
Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies.
Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: 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 / _citation_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
A: exo-2S-iota carrageenan S1 sulfatase
B: exo-2S-iota carrageenan S1 sulfatase
C: exo-2S-iota carrageenan S1 sulfatase
D: exo-2S-iota carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,73549
Polymers226,6514
Non-polymers4,08445
Water33,2021843
1
A: exo-2S-iota carrageenan S1 sulfatase
B: exo-2S-iota carrageenan S1 sulfatase
hetero molecules

A: exo-2S-iota carrageenan S1 sulfatase
B: exo-2S-iota carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,64348
Polymers226,6514
Non-polymers3,99244
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16170 Å2
ΔGint-235 kcal/mol
Surface area62940 Å2
MethodPISA
2
C: exo-2S-iota carrageenan S1 sulfatase
D: exo-2S-iota carrageenan S1 sulfatase
hetero molecules

C: exo-2S-iota carrageenan S1 sulfatase
D: exo-2S-iota carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,82750
Polymers226,6514
Non-polymers4,17646
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area16500 Å2
ΔGint-238 kcal/mol
Surface area62220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.830, 110.680, 175.900
Angle α, β, γ (deg.)90.000, 105.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1090-

HOH

21A-1137-

HOH

31B-1104-

HOH

41B-1148-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24D
15B
25C
16B
26D
17B
27D
18C
28D
19C
29D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA36 - 50726 - 497
21LEULEUBB36 - 50726 - 497
12LEULEUAA36 - 50726 - 497
22LEULEUCC36 - 50726 - 497
13ALAALAAA36 - 41326 - 403
23ALAALADD36 - 41326 - 403
14PHEPHEAA415 - 506405 - 496
24PHEPHEDD415 - 506405 - 496
15LEULEUBB36 - 50726 - 497
25LEULEUCC36 - 50726 - 497
16ALAALABB36 - 41326 - 403
26ALAALADD36 - 41326 - 403
17PHEPHEBB415 - 506405 - 496
27PHEPHEDD415 - 506405 - 496
18ALAALACC36 - 41326 - 403
28ALAALADD36 - 41326 - 403
19PHEPHECC415 - 506405 - 496
29PHEPHEDD415 - 506405 - 496

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
exo-2S-iota carrageenan S1 sulfatase


Mass: 56662.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Strain: PS47 / Gene: EU509_08820 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A063KNC1*PLUS
#4: Sugar
ChemComp-G4S / 4-O-sulfo-beta-D-galactopyranose / 4-O-sulfo-beta-D-galactose / 4-O-sulfo-D-galactose / 4-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 260.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O9S
IdentifierTypeProgram
DGalp[4S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
4-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-Galp4SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 1884 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-9RN / 3,6-anhydro-D-galactose


Mass: 162.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H10O5
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1843 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Na cacodylate, Ca acetate, LiCl2, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→68.78 Å / Num. obs: 201748 / % possible obs: 87 % / Redundancy: 4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.8
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.202 / Num. unique obs: 28359

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0253refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PT4

6pt4


Resolution: 1.75→56.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.605 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.091
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1625 10249 5.1 %RANDOM
Rwork0.1396 ---
obs0.1407 191489 87.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 53.81 Å2 / Biso mean: 13.625 Å2 / Biso min: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.45 Å2
2---1.01 Å20 Å2
3---0.57 Å2
Refinement stepCycle: final / Resolution: 1.75→56.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15068 0 232 1843 17143
Biso mean--19.21 23.25 -
Num. residues----1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01315749
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713935
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.65921345
X-RAY DIFFRACTIONr_angle_other_deg1.5021.58732421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95551892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95922.46866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.746152550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5891596
X-RAY DIFFRACTIONr_chiral_restr0.1250.21968
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023353
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A167550.04
12B167550.04
21A167860.04
22C167860.04
31A130540.04
32D130540.04
41A31250.03
42D31250.03
51B167750.04
52C167750.04
61B131180.04
62D131180.04
71B31210.04
72D31210.04
81C130530.04
82D130530.04
91C31470.04
92D31470.04
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 740 -
Rwork0.17 13646 -
all-14386 -
obs--84.3 %

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