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- PDB-6b0j: Crystal structure of Ps i-CgsB in complex with k-i-k-neocarrahexaose -

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Basic information

Entry
Database: PDB / ID: 6b0j
TitleCrystal structure of Ps i-CgsB in complex with k-i-k-neocarrahexaose
ComponentsIota-carrageenan sulfatase
KeywordsHYDROLASE / S1 sulfatase
Function / homologysulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / 3,6-anhydro-D-galactose / ARGININE / 4-O-sulfo-beta-D-galactopyranose / Sulfatase
Function and homology information
Biological speciesPseudoalteromonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHettle, A.G. / Boraston, A.B.
CitationJournal: Structure / Year: 2018
Title: The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme.
Authors: Hettle, A.G. / Vickers, C. / Robb, C.S. / Liu, F. / Withers, S.G. / Hehemann, J.H. / Boraston, A.B.
History
DepositionSep 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
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 4, 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: Iota-carrageenan sulfatase
B: Iota-carrageenan sulfatase
C: Iota-carrageenan sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,16227
Polymers154,0163
Non-polymers6,14624
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint15 kcal/mol
Surface area48960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.390, 123.390, 240.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA28 - 4771 - 450
21LYSLYSBB28 - 4771 - 450
12LYSLYSAA28 - 4771 - 450
22LYSLYSCC28 - 4771 - 450
13THRTHRBB28 - 4781 - 451
23THRTHRCC28 - 4781 - 451

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Iota-carrageenan sulfatase


Mass: 51338.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A063KPH1*PLUS

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Sugars , 3 types, 8 molecules

#2: Polysaccharide
4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O- ...4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 726.612 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2112h-1b_1-5_4*OSO/3=O/3=O][a2112h-1a_1-5_3-6_2*OSO/3=O/3=O]/1-2-1/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
#3: 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.: 1
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
#5: 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.: 3
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, 255 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 162.141 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C6H10O5
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.65 / Details: PEG 3350, citric acid, arginine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→109.8 Å / Num. obs: 63124 / CC1/2: 0.992 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.067
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9074 / Num. unique obs: 63124 / CC1/2: 0.778 / Rpim(I) all: 0.311 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HDH

1hdh


Resolution: 2.5→109.75 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.064 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.48 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 3136 5 %RANDOM
Rwork0.2145 ---
obs0.2155 59927 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.89 Å2 / Biso mean: 27.894 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.5→109.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10625 0 376 239 11240
Biso mean--41.25 19.52 -
Num. residues----1354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911377
X-RAY DIFFRACTIONr_bond_other_d0.0020.029774
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.96615508
X-RAY DIFFRACTIONr_angle_other_deg0.956322811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97351361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95824.376537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.813151705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9721546
X-RAY DIFFRACTIONr_chiral_restr0.0770.21671
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022323
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
11A30672
12B30672
21A30674
22C30674
31B30804
32C30804
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 228 -
Rwork0.279 4380 -
all-4608 -
obs--97.32 %

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