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- PDB-2nx7: Structure of NOWA cysteine rich domain 8 -

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Basic information

Entry
Database: PDB / ID: 2nx7
TitleStructure of NOWA cysteine rich domain 8
ComponentsNematocyst outer wall antigen
KeywordsSTRUCTURAL PROTEIN / cysteine rich / disulfide bonds / rich in turns
Function / homology
Function and homology information


Golgi-associated plant pathogenesis-related protein 1, SCP domain / : / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / SEA domain / SEA domain / Lectin C-type domain / C-type lectin domain profile. ...Golgi-associated plant pathogenesis-related protein 1, SCP domain / : / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / SEA domain / SEA domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Nematocyst outer wall antigen
Similarity search - Component
Biological speciesHydra vulgaris (swiftwater hydra)
MethodSOLUTION NMR / simulated annealing
AuthorsMeier, S. / Jensen, P.R. / Adamczyk, P. / Bachinger, H.P. / Holstein, T.W. / Engel, J. / Ozbek, S. / Grzesiek, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Sequence-structure and structure-function analysis in cysteine-rich domains forming the ultrastable nematocyst wall.
Authors: Meier, S. / Jensen, P.R. / Adamczyk, P. / Bachinger, H.P. / Holstein, T.W. / Engel, J. / Ozbek, S. / Grzesiek, S.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nematocyst outer wall antigen


Theoretical massNumber of molelcules
Total (without water)2,7571
Polymers2,7571
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 Nematocyst outer wall antigen


Mass: 2757.177 Da / Num. of mol.: 1 / Fragment: domain 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Gene: NOWA / Plasmid: pGEV2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IT70
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
1313D 15N-separated ROESY
14115N HSQC
NMR detailsText: 800 Mhz with TCI probe

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Sample preparation

DetailsContents: 0.5 mM peptide, pH 5.5, 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 20 mM / pH: 5.5 / 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 DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger A. T. et alrefinement
NMRPipe2.1Delaglio et alprocessing
XwinNMR3.5BRUKERcollection
PIPP4.3.2Garrett D. et aldata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
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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