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- PDB-1sp7: Structure of the Cys-rich C-terminal domain of Hydra minicollagen -

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Basic information

Entry
Database: PDB / ID: 1sp7
TitleStructure of the Cys-rich C-terminal domain of Hydra minicollagen
Componentsmini-collagen
KeywordsSTRUCTURAL PROTEIN / cysteine-rich / proline-rich / disulfide bond
Function / homologyMinicollagen I, C-terminal domain / collagen trimer / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Mini-collagen
Function and homology information
MethodSOLUTION NMR / simulated annealing with torsion angle dynamics
AuthorsMeier, S. / Haussinger, D. / Pokidysheva, E. / Bachinger, H.P. / Grzesiek, S.
Citation
Journal: Febs Lett. / Year: 2004
Title: Determination of a high-precision NMR structure of the minicollagen cysteine rich domain from Hydra and characterization of its disulfide bond formation.
Authors: Meier, S. / Haussinger, D. / Pokidysheva, E. / Bachinger, H.P. / Grzesiek, S.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: The structure of the Cys-rich terminal domain of Hydra minicollagen, which is involved in disulfide networks of the nematocyst wall.
Authors: Pokidysheva, E. / Milbradt, A.G. / Meier, S. / Renner, C. / Haussinger, D. / Bachinger, H.P. / Moroder, L. / Grzesiek, S. / Holstein, T.W. / Ozbek, S. / Engel, J.
History
DepositionMar 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mini-collagen


Theoretical massNumber of molelcules
Total (without water)2,5951
Polymers2,5951
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
Representative

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Components

#1: Protein/peptide mini-collagen


Mass: 2595.198 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence occurs naturally in Hydra sp.
References: UniProt: Q00484
Has protein modificationY

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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
1422D TOCSY
NMR detailsText: natural abundance spectra for RDCs and TALOS

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Sample preparation

Details
Solution-IDContentsSolvent system
16 mM MCRD90 % H2O, 10 % D2O, 5 mM phosphate pH 6.5
22 mM MCRD100 % D2O, 5 mM phosphate pH 6.5
Sample conditionsIonic strength: ~15 mM / pH: 6.5 / Pressure: ambient / Temperature: 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 DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Delaglio et al.data analysis
PIPP4.3.2Garrett et al.data analysis
CNS1Brunger et al.structure solution
CNS1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
RefinementMethod: simulated annealing with torsion angle dynamics / Software ordinal: 1 / Details: standard CNS protocol
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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