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- PDB-2hm3: Nematocyst outer wall antigen, cysteine rich domain NW1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2hm3
TitleNematocyst outer wall antigen, cysteine rich domain NW1
ComponentsNematocyst outer wall antigen
KeywordsSTRUCTURAL PROTEIN / disulfide / evolution / cysteine rich / nematocyst
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 / CAP superfamily / Cysteine-rich secretory protein family / SEA domain / SEA domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like ...Golgi-associated plant pathogenesis-related protein 1, SCP domain / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / 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. / Grzesiek, S. / Oezbek, S.
Citation
Journal: 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.
#1: Journal: Curr.Biol. / Year: 2007
Title: Continuous molecular evolution of protein-domain structures by single amino Acid changes.
Authors: Meier, S. / Jensen, P.R. / David, C.N. / Chapman, J. / Holstein, T.W. / Grzesiek, S. / Ozbek, S.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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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)3,0801
Polymers3,0801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #3lowest energy

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Components

#1: Protein/peptide Nematocyst outer wall antigen


Mass: 3080.433 Da / Num. of mol.: 1 / Fragment: First cysteine rich domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IT70

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1323D 15N-separated ROESY
142HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM NW1 unlabelled, 5 mM phosphate buffer, 95% H2O, 5% D2O95% H2O/5% D2O
20.6 mM NW1 U-15N, 5 mM phosphate buffer, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 10 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
CNS1.1Br ngerstructure solution
NMRPipe2.1Delaglioprocessing
PIPP4.3.2Garrettdata analysis
XwinNMR3.5Brukercollection
CNS1.1Br ngerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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