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- PDB-5l1m: CASKIN2 SAM domain tandem -

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Basic information

Entry
Database: PDB / ID: 5l1m
TitleCASKIN2 SAM domain tandem
ComponentsCaskin-2
KeywordsPROTEIN BINDING / signaling protein / protein interaction domain / sterile alpha motif
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 / : / Transcription Factor, Ets-1 ...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 / : / Transcription Factor, Ets-1 / Variant SH3 domain / SAM domain (Sterile alpha motif) / 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 / Src homology 3 domains / DNA polymerase; domain 1 / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.751 Å
AuthorsDonaldson, L.W. / Kwan, J.J. / Saridakis, V.
CitationJournal: Cell Commun. Signal / Year: 2016
Title: A new mode of SAM domain mediated oligomerization observed in the CASKIN2 neuronal scaffolding protein.
Authors: Smirnova, E. / Kwan, J.J. / Siu, R. / Gao, X. / Zoidl, G. / Demeler, B. / Saridakis, V. / Donaldson, L.W.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_database_PDB_obs_spr / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Feb 8, 2023Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 2023Group: 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)20,3071
Polymers20,3071
Non-polymers00
Water00
1
A: Caskin-2

A: Caskin-2


Theoretical massNumber of molelcules
Total (without water)40,6142
Polymers40,6142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area3470 Å2
ΔGint-21 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.460, 96.460, 119.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsDimer according to Gel filtration and Analytical ultracentrifuge

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Components

#1: Protein Caskin-2 / CASK-interacting protein 2


Mass: 20307.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASKIN2, KIAA1139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXE0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris pH 7.5, 2.4 M sodium formate, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97912 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.75→48.51 Å / Num. obs: 9004 / % possible obs: 100 % / Redundancy: 1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 56.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.751→48.509 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.32
RfactorNum. reflection% reflection
Rfree0.2649 901 10.01 %
Rwork0.2449 --
obs0.2471 9004 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.751→48.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 0 0 1100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121135
X-RAY DIFFRACTIONf_angle_d1.2691540
X-RAY DIFFRACTIONf_dihedral_angle_d12.944674
X-RAY DIFFRACTIONf_chiral_restr0.065173
X-RAY DIFFRACTIONf_plane_restr0.006194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7505-2.92290.35911460.32291312X-RAY DIFFRACTION100
2.9229-3.14850.36921450.33011307X-RAY DIFFRACTION100
3.1485-3.46530.34691470.27891325X-RAY DIFFRACTION100
3.4653-3.96650.31011490.251335X-RAY DIFFRACTION100
3.9665-4.99660.22971510.22041360X-RAY DIFFRACTION100
4.9966-48.51690.22941630.22831464X-RAY DIFFRACTION100

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