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- PDB-2rvf: Solution NMR structure of Monosiga brevicollis CRK/CRKL homolog (... -

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Basic information

Entry
Database: PDB / ID: 2rvf
TitleSolution NMR structure of Monosiga brevicollis CRK/CRKL homolog (crka1) SH2 domain
ComponentsPredicted proteinProtein structure prediction
KeywordsSIGNALING PROTEIN / signal transduction / phosphotyrosine-binding domain
Function / homology
Function and homology information


SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMonosiga brevicollis (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailsminimized average structure, model1 and lowest energy, model2-21
Model type detailsminimized average
AuthorsKasai, T. / Pawlak, J. / Imamoto, A. / Kigawa, T.
CitationJournal: Sci Rep / Year: 2016
Title: A pre-metazoan origin of the CRK gene family and co-opted signaling network
Authors: Shigeno-Nakazawa, Y. / Kasai, T. / Ki, S. / Kostyanovskaya, E. / Pawlak, J. / Yamagishi, J. / Okimoto, N. / Taiji, M. / Okada, M. / Westbrook, J. / Satta, Y. / Kigawa, T. / Imamoto, A.
History
DepositionSep 24, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted protein


Theoretical massNumber of molelcules
Total (without water)11,4831
Polymers11,4831
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)21 / 100target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Predicted protein / Protein structure prediction


Mass: 11482.659 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monosiga brevicollis (eukaryote) / Gene: 25438, crka1 / Production host: cell-free protein synthesis (unknown) / References: UniProt: A9UZF4*PLUS
Sequence detailsADDITIONAL N-TERMINAL GSSGSSG ARE CLONING ARTIFACTS. PREDICTED PROTEIN IS RESIDUES 1-97. THE ...ADDITIONAL N-TERMINAL GSSGSSG ARE CLONING ARTIFACTS. PREDICTED PROTEIN IS RESIDUES 1-97. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THIS PROTEIN HAS THE SEQUENCE, WHICH IS ASSIGNED TO THE GENEBANK ID KT795324.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CO
1513D HNCA
1613D HN(CO)CA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HBHA(CO)NH
11013D C(CO)NH
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY
11312D (HB)CB(CGCD)HD
11413D 1H-15N NOESY
11513D 1H-13C NOESY
NMR detailsText: THE FIRST MODEL 1 IS THE ENERGY-MINIMIZED MEAN STRUCTURE CALCULATED FROM THE OTHER 20 STRUCTURES.

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Sample preparation

DetailsContents: 1.1 mM [U-13C; U-15N] crka1 SH2 domain-1, 20 mM [U-2H] TRIS-2, 100 mM sodium chloride-3, 0.02 % sodium azide-4, 1 mM [U-2H] DTT-5, 10 % [U-2H] D2O-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMcrka1 SH2 domain-1[U-13C; U-15N]1
20 mMTRIS-2[U-2H]1
100 mMsodium chloride-31
0.02 %sodium azide-41
1 mMDTT-5[U-2H]1
10 %D2O-6[U-2H]1
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Bruker Biospincollection
TopSpin2.1Bruker Biospincollection
NMRPipe20110801Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2_01Johnson, One Moon Scientificdata analysis
KUJIRA0.9843Kobayashi, Iwahara, Koshiba, Tomizawa, Tochio, G ntert, Kigawa, Yokoyamadata analysis
KUJIRA0.9843Kobayashi, Iwahara, Koshiba, Tomizawa, Tochio, G ntert, Kigawa, Yokoyamachemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANArefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 21 / Representative conformer: 1

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