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- PDB-2oq9: Structure of the non-canonical Mcol5 of Hydra nematocysts -

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Basic information

Entry
Database: PDB / ID: 2oq9
TitleStructure of the non-canonical Mcol5 of Hydra nematocysts
ComponentsMinicollagen-5
KeywordsSTRUCTURAL PROTEIN / disulfide / cis-proline / nematocyst / non-canonical CRD / cysteine-rich domain
Function / homologynematocyst / collagen trimer / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Minicollagen-15
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsMeier, S. / Oezbek, S. / Grzesiek, S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Minicollagen-15, a novel minicollagen isolated from Hydra, forms tubule structures in nematocysts.
Authors: Adamczyk, P. / Meier, S. / Gross, T. / Hobmayer, B. / Grzesiek, S. / Bachinger, H.P. / Holstein, T.W. / Ozbek, S.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minicollagen-5


Theoretical massNumber of molelcules
Total (without water)2,3641
Polymers2,3641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Minicollagen-5


Mass: 2363.822 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: wild type sequence obtained by solid phase synthesis and oxidative refolding
References: UniProt: A6N8P1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D NOESY
131HSQC
242IPAP
NMR detailsText: This structure was determined using standard 2D homonuclear and weak alignment techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
14 mM peptide; 95% H2O, 5% D2O95% H2O/5% D2O
23 mM peptide, 10 mg/ml Pf1 phage; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM 4.5 ambient 288 K
255 mM 5.5 ambient 288 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 DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger A. T. et alstructure solution
NMRPipe2.1Delaglio et alprocessing
PIPP4.3.2Garrettdata analysis
XwinNMR3.5Brukercollection
CNS1Brunger A. T. et alrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: use of RDCs with the ISAC procedure, no a priori knowledge of the alignment tensor
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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