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- PDB-2a05: The cysteine-rich secretory protein domain of Tpx-1 is related to... -

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Basic information

Entry
Database: PDB / ID: 2a05
TitleThe cysteine-rich secretory protein domain of Tpx-1 is related to ion channel toxins and regulates Ryanodine receptor Ca2+ signaling
ComponentsCysteine-rich secretory protein-2
KeywordsSIGNALING PROTEIN / 3 Alpha Helices / 5 Disulphide bonds / 2 domains
Function / homology
Function and homology information


cell-cell adhesion / extracellular space
Similarity search - Function
Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain ...Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain / ShKT domain profile. / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cysteine-rich secretory protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / Automated Resonance assignment using Torsion Angle Dynamics (CANDID), Further refinement with CA, CB chem shifts, database potentials
AuthorsGibbs, G.M. / Scanlon, M.J. / Swarbrick, J. / Curtis, S. / Dulhunty, A.F. / O'Bryan, M.K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The cysteine-rich secretory protein domain of Tpx-1 is related to ion channel toxins and regulates ryanodine receptor Ca2+ signaling.
Authors: Gibbs, G.M. / Scanlon, M.J. / Swarbrick, J. / Curtis, S. / Gallant, E. / Dulhunty, A.F. / O'Bryan, M.K.
History
DepositionJun 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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: Cysteine-rich secretory protein-2


Theoretical massNumber of molelcules
Total (without water)6,1221
Polymers6,1221
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)23 / 49violations <0.2A NOE, total energy
RepresentativeModel #1lowest target function

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Components

#1: Protein Cysteine-rich secretory protein-2 / Tpx-1 Crisp / CRISP-2 / Testis-specific protein TPX-1


Mass: 6121.932 Da / Num. of mol.: 1 / Fragment: residues 189-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pTriEx4 / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE3) pLacI / References: UniProt: P16563

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
1322D NOESY
1432D TOCSY
153DQF-COSY
1632D NOESY
NMR detailsText: Standard 2D/3D methods

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Sample preparation

Details
Solution-IDContents
11mM TpX-1 U-15N 90% H2O 10% D2O
21mM TpX-1 90% H2O 10% D2O
31mM TpX-1 100% D2O
Sample conditionsIonic strength: 1mM / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1Brukercollection
XwinNMR1Brukerprocessing
Sparky3.101Goddard Kellerdata analysis
CYANA1.06Guntertrefinement
XPLOR-NIH2.9.9Clore Schwieters Kuszewski Tjandrarefinement
RefinementMethod: Automated Resonance assignment using Torsion Angle Dynamics (CANDID), Further refinement with CA, CB chem shifts, database potentials
Software ordinal: 1
Details: NOES: 187 intra 251 short 253 med 188 long. 78 Chem shifts
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: violations <0.2A NOE, total energy / Conformers calculated total number: 49 / Conformers submitted total number: 23

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