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- PDB-1sop: C-terminal cystine-rich domain of Minicollagen-I from Hydra -

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Basic information

Entry
Database: PDB / ID: 1sop
TitleC-terminal cystine-rich domain of Minicollagen-I from Hydra
Componentsmini-collagen
KeywordsSTRUCTURAL PROTEIN / collagen oxidative refolding
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 / Distance Geometry MD refinement
AuthorsMilbradt, A.G. / Moroder, L. / Renner, C.
CitationJournal: 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 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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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)2,6191
Polymers2,6191
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 mini-collagen


Mass: 2619.243 Da / Num. of mol.: 1 / Fragment: c-terminal cystine-rich Domain / Source method: obtained synthetically
Details: Fmoc solid phase synthesis + oxidation. The sequence is naturally found in Hydra sp.
References: UniProt: Q00484

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
141ROESY

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Sample preparation

DetailsContents: 3 mM peptide / Solvent system: water
Sample conditionsIonic strength: 10 mM / pH: 3.5 / Pressure: 1 bar / Temperature: 283 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 DRXBrukerDRX5001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX9003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3brukercollection
DGIIinsight 2000msistructure solution
Discover2.98msirefinement
RefinementMethod: Distance Geometry MD refinement / Software ordinal: 1
Details: Independent DG structures subsequently refined by MDSA experimental restraints applied throughout
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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