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- PDB-6psm: Crystal structure of PsS1_19B C77S in complex with kappa-neocarrabiose -

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Basic information

Entry
Database: PDB / ID: 6psm
TitleCrystal structure of PsS1_19B C77S in complex with kappa-neocarrabiose
Componentsexo-4S-kappa carrageenan S1 sulfatase
KeywordsHYDROLASE / S1 sulfatase
Function / homologysulfuric ester hydrolase activity / Sulfatases signature 1. / Sulfatase, conserved site / 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: 1.95 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 12, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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-4S-kappa carrageenan S1 sulfatase
B: exo-4S-kappa carrageenan S1 sulfatase
C: exo-4S-kappa carrageenan S1 sulfatase
D: exo-4S-kappa carrageenan S1 sulfatase
E: exo-4S-kappa carrageenan S1 sulfatase
F: exo-4S-kappa carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,00041
Polymers318,3106
Non-polymers3,69035
Water15,961886
1
A: exo-4S-kappa carrageenan S1 sulfatase
B: exo-4S-kappa carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,29213
Polymers106,1032
Non-polymers1,18911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-42 kcal/mol
Surface area29770 Å2
MethodPISA
2
C: exo-4S-kappa carrageenan S1 sulfatase
E: exo-4S-kappa carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,35414
Polymers106,1032
Non-polymers1,25112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-34 kcal/mol
Surface area30130 Å2
MethodPISA
3
D: exo-4S-kappa carrageenan S1 sulfatase
F: exo-4S-kappa carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,35414
Polymers106,1032
Non-polymers1,25112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-43 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.050, 93.050, 300.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROAA27 - 47323 - 469
21SERSERPROPROBB27 - 47323 - 469
12SERSERGLNGLNAA27 - 47223 - 468
22SERSERGLNGLNCC27 - 47223 - 468
13SERSERPROPROAA27 - 47323 - 469
23SERSERPROPRODD27 - 47323 - 469
14SERSERGLNGLNAA27 - 47223 - 468
24SERSERGLNGLNEE27 - 47223 - 468
15SERSERPROPROAA27 - 47323 - 469
25SERSERPROPROFF27 - 47323 - 469
16SERSERGLNGLNBB27 - 47223 - 468
26SERSERGLNGLNCC27 - 47223 - 468
17SERSERPROPROBB27 - 47323 - 469
27SERSERPROPRODD27 - 47323 - 469
18SERSERGLNGLNBB27 - 47223 - 468
28SERSERGLNGLNEE27 - 47223 - 468
19SERSERPROPROBB27 - 47323 - 469
29SERSERPROPROFF27 - 47323 - 469
110SERSERPROPROCC27 - 47323 - 469
210SERSERPROPRODD27 - 47323 - 469
111ALAALAPROPROCC26 - 47322 - 469
211ALAALAPROPROEE26 - 47322 - 469
112ALAALAPROPROCC26 - 47322 - 469
212ALAALAPROPROFF26 - 47322 - 469
113SERSERPROPRODD27 - 47323 - 469
213SERSERPROPROEE27 - 47323 - 469
114SERSERPROPRODD27 - 47323 - 469
214SERSERPROPROFF27 - 47323 - 469
115ALAALAPROPROEE26 - 47322 - 469
215ALAALAPROPROFF26 - 47322 - 469

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
exo-4S-kappa carrageenan S1 sulfatase


Mass: 53051.590 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Strain: PS47 / Gene: EU509_08890 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A063KLJ9*PLUS
#3: 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.: 6 / Source method: obtained synthetically / Formula: C6H12O9S / Feature type: SUBJECT OF INVESTIGATION
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, 915 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-9RN / 3,6-anhydro-D-galactose


Mass: 162.141 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10O5
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ZnCl2, gly-gly, 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: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→48.19 Å / Num. obs: 211230 / % possible obs: 99.7 % / Redundancy: 11.6 % / CC1/2: 0.995 / Net I/σ(I): 12.6
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 1.178 / Num. unique obs: 10521 / CC1/2: 0.824

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6prm


Resolution: 1.95→48.19 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.878 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.14
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 10434 4.9 %RANDOM
Rwork0.1924 ---
obs0.1934 200795 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.37 Å2 / Biso mean: 19.38 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----2.44 Å2
Refinement stepCycle: final / Resolution: 1.95→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21147 0 194 886 22227
Biso mean--19.74 19.96 -
Num. residues----2681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01321906
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719692
X-RAY DIFFRACTIONr_angle_refined_deg1.431.66429628
X-RAY DIFFRACTIONr_angle_other_deg1.3141.59145810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21452680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40722.5321181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.868153620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.65515132
X-RAY DIFFRACTIONr_chiral_restr0.070.22714
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024750
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A15407
12B15407
21A15361
22C15361
31A15263
32D15263
41A15383
42E15383
51A15360
52F15360
61B15354
62C15354
71B15243
72D15243
81B15295
82E15295
91B15284
92F15284
101C15220
102D15220
111C15384
112E15384
121C15276
122F15276
131D15260
132E15260
141D15213
142F15213
151E15345
152F15345
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 740 -
Rwork0.243 14821 -
all-15561 -
obs--99.17 %

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