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- PDB-4b1q: NMR structure of the glycosylated conotoxin CcTx from Conus consors -

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Basic information

Entry
Database: PDB / ID: 4b1q
TitleNMR structure of the glycosylated conotoxin CcTx from Conus consors
ComponentsCONOTOXIN CCTX
KeywordsTOXIN / O-GLYCAN
Function / homologytoxin activity / extracellular region / Conotoxin CcTx
Function and homology information
Biological speciesCONUS CONSORS (invertebrata)
MethodSOLUTION NMR / CYANA, CNS
AuthorsHocking, H.G. / Gerwig, G.J. / Favreau, P. / Stocklin, R. / Kamerling, J.P. / Boelens, R.
CitationJournal: Chemistry / Year: 2013
Title: Structure of the O-Glycosylated Conopeptide Cctx from Conus Consors Venom.
Authors: Hocking, H.G. / Gerwig, G.J. / Dutertre, S. / Violette, A. / Favreau, P. / Stocklin, R. / Kamerling, J.P. / Boelens, R.
History
DepositionJul 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: CONOTOXIN CCTX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1432
Polymers3,2321
Non-polymers9111
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein/peptide CONOTOXIN CCTX / EXCITOTOXIN CCTX / KAPPAA-CONOTOXIN


Mass: 3231.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CONUS CONSORS (invertebrata) / References: UniProt: P58928
#2: Polysaccharide alpha-L-galactopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-galactopyranose-(1-4)-2- ...alpha-L-galactopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LGalpa1-2DGalpb1-3[LGalpa1-4DGlcpNAca1-6]DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O]/1-2-3-4-3/a3-b1_a6-d1_b2-c1_d4-e1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Galp]{}}[(6+1)][a-D-GlcpNAc]{[(4+1)][a-L-Galp]{}}}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
141H2BC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING NOE RESTRAINTS ORIGINATING FROM BOTH THE PEPTIDE AND GLYCAN COMPONENTS OF THE SYSTEM.

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Sample preparation

DetailsContents: 95 % H2O/ 5% D2O
Sample conditionspH: 3.0 / Temperature: 292.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CcpNmr AnalysisANALYSISstructure solution
RefinementMethod: CYANA, CNS / Software ordinal: 1 / Details: REFINEMENT IN EXPLICIT WATER SOLVENT
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 200 / Conformers submitted total number: 20

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