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- PDB-6pt6: Crystal structure of PsS1_NC C84S in complex with i-neocarratetraose -

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Basic information

Entry
Database: PDB / ID: 6pt6
TitleCrystal structure of PsS1_NC C84S in complex with i-neocarratetraose
Componentsexo-2S-iota 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 / Sulfatase
Function and homology information
Biological speciesPseudoalteromonas fuliginea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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 15, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,4066
Polymers113,3572
Non-polymers1,0494
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-18 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.728, 102.211, 170.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B35 - 507
2010A35 - 507

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Components

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


Mass: 56678.719 Da / Num. of mol.: 2
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
#2: Polysaccharide 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 484.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_4*OSO/3=O/3=O][a2112h-1a_1-5_3-6_2*OSO/3=O/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp4SO3]{[(3+1)]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Hepes, sodium acetate trihydrate, arginine, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 46858 / % possible obs: 95.3 % / Redundancy: 4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.6
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.292 / Num. unique obs: 4243

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0253refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PT4

6pt4


Resolution: 2.25→31.78 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.017 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 2387 5 %RANDOM
Rwork0.2002 ---
obs0.2027 45724 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.47 Å2 / Biso mean: 30.727 Å2 / Biso min: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.17 Å20 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 2.25→31.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7513 0 57 312 7882
Biso mean--53.28 29.22 -
Num. residues----945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137808
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176859
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.6610599
X-RAY DIFFRACTIONr_angle_other_deg1.351.58815967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4285944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08122.454432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.051151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5911548
X-RAY DIFFRACTIONr_chiral_restr0.0780.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021674
Refine LS restraints NCS

Ens-ID: 1 / Number: 16190 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.251→2.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 173 -
Rwork0.244 3275 -
all-3448 -
obs--96.1 %

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