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- PDB-2ke9: NMR solution structure of the CASKIN SH3 domain -

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Basic information

Entry
Database: PDB / ID: 2ke9
TitleNMR solution structure of the CASKIN SH3 domain
ComponentsCaskin-2
KeywordsPROTEIN BINDING / SH3 domain / ANK repeat / Cytoplasm / Phosphoprotein
Function / homology
Function and homology information


Caskin2, SH3 domain / Caskin, C-terminal / Caskin-1, CASK-interaction domain / Caskin1/2, SAM repeat 1 / Caskin1/2, SAM repeat 2 / Caskin1 CASK-interaction domain / C-terminal region of Caskin / Proline rich region of Caskin proteins / : / Variant SH3 domain ...Caskin2, SH3 domain / Caskin, C-terminal / Caskin-1, CASK-interaction domain / Caskin1/2, SAM repeat 1 / Caskin1/2, SAM repeat 2 / Caskin1 CASK-interaction domain / C-terminal region of Caskin / Proline rich region of Caskin proteins / : / Variant SH3 domain / SAM domain (Sterile alpha motif) / SH3 Domains / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, water refinement
AuthorsDonaldson, L.
CitationJournal: To be Published
Title: NMR solution structure of the CASKIN SH3 domain
Authors: Donaldson, L.
History
DepositionJan 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: 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 / 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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caskin-2


Theoretical massNumber of molelcules
Total (without water)9,3431
Polymers9,3431
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)15 / 25
RepresentativeModel #1lowest energy

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Components

#1: Protein Caskin-2


Mass: 9343.499 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: amino terminal His6 affinity tag and intervening thrombin site
Gene: CASKIN2, KIAA1139 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21(DE3) / References: UniProt: Q8WXE0

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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 CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.6 mM [U-98% 13C; U-98% 15N] caskinSH3-1, 10 mM D2O-2, 0.05 % sodium azide-3, 150 mM sodium chloride-4, 20 mM sodium phosphate-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMcaskinSH3-1[U-98% 13C; U-98% 15N]1
10 mMD2O-21
0.05 %sodium azide-31
150 mMsodium chloride-41
20 mMsodium phosphate-51
Sample conditionsIonic strength: 0.15 / pH: 7.8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian NMRS / Manufacturer: Varian / Model: NMRS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, P. et al.structure solution
NMRView5.1Johnson, B. et al.peak picking
X-PLOR NIH2.21Schwieters, C.D. et al.refinement
RefinementMethod: torsion angle dynamics, water refinement / Software ordinal: 1
Details: CYANA 2.1 was used to determine 250 initial solutions of which 25 were selected as the initial ensemble. 5000 steps of torsion angle dynamics were performed, XPLOR-NIH 2.21 was used to ...Details: CYANA 2.1 was used to determine 250 initial solutions of which 25 were selected as the initial ensemble. 5000 steps of torsion angle dynamics were performed, XPLOR-NIH 2.21 was used to further refine the 25 structure in explicit solvent. 2000 hot steps at 500 K were performed followed by 500 cool steps down to 100 K in 100 K steps.
NMR constraintsNOE constraints total: 445 / NOE intraresidue total count: 204 / NOE long range total count: 127 / NOE medium range total count: 12 / NOE sequential total count: 102
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 25 / Conformers submitted total number: 15 / Maximum lower distance constraint violation: 0.5 Å / Maximum upper distance constraint violation: 0.5 Å

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