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- PDB-2hgo: NMR structure of Cassiicolin -

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Basic information

Entry
Database: PDB / ID: 2hgo
TitleNMR structure of Cassiicolin
ComponentsCASSIICOLIN
KeywordsTOXIN / DISULFIDE BRIDGE / GLYCOPROTEIN
Function / homologytoxin activity / extracellular region / 1,5-anhydro-3-O-methyl-D-mannitol / Cassiicolin
Function and homology information
Biological speciesCorynespora cassiicola (fungus)
MethodSOLUTION NMR / distance geometry
AuthorsBarthe, P. / Pujade-Renault, V. / Roumestand, C. / de Lamotte, F.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Analysis of Cassiicolin, a Host-selective Protein Toxin from Corynespora cassiicola
Authors: Barthe, P. / Pujade-Renaud, V. / Breton, F. / Gargani, D. / Thai, R. / Roumestand, C. / de Lamotte, F.
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_nmr_software ...entity_poly / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Assembly

Deposited unit
A: CASSIICOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8952
Polymers2,7171
Non-polymers1781
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide CASSIICOLIN


Mass: 2716.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynespora cassiicola (fungus) / Production host: Corynespora cassiicola (fungus) / References: UniProt: P84902
#2: Sugar ChemComp-3HD / 1,5-anhydro-3-O-methyl-D-mannitol


Type: D-saccharide / Mass: 178.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1322D NOESY
142DQF-COSY
2512D 15N-separated HSQC
3622D 13C-separated HSQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and 15N and 13C HSQC in natural abundance. Threonine 2 is glycosylated by a 3-O-methyl-alpha-D-mannose.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Cassiicolin, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM Cassiicolin, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 3.3 ambient 290 K
20 3.3 ambient 300 K
30 3.3 ambient 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
Gifa4.4Delsucprocessing
CINDY1.5Padilladata analysis
CYANA2.1Guntertstructure solution
CNS1.1Brungerrefinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: The structures are based on a total of 274 restraints: 220 are NOE-derived distance constraints, 36 are dihedral angle restraints, and 18 are distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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