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- PDB-4is7: Crystal Structure of the CASKIN2 SAM Domain Tandem -

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Basic information

Entry
Database: PDB / ID: 4is7
TitleCrystal Structure of the CASKIN2 SAM Domain Tandem
ComponentsCaskin-2
KeywordsPROTEIN BINDING / sterile alpha motif / scaffolding protein / SAM domain
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 / Resolution: 2.751 Å
AuthorsDonaldson, L.W. / Kwan, J.J.
CitationJournal: To be Published
Title: Crystal Structure of the CASKIN2 SAM Domain Tandem
Authors: J., Kwan J. / Smirnova, E. / Saridakis, V. / Donaldson, L.W.
History
DepositionJan 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caskin-2


Theoretical massNumber of molelcules
Total (without water)18,9991
Polymers18,9991
Non-polymers00
Water00
1
A: Caskin-2

A: Caskin-2


Theoretical massNumber of molelcules
Total (without water)37,9972
Polymers37,9972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area3470 Å2
ΔGint-23 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.460, 96.460, 119.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Detailsbiological unit is the same as asym.

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Components

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


Mass: 18998.607 Da / Num. of mol.: 1 / Fragment: UNP residues 483-633
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASKIN2, KIAA1139 / Plasmid: pET28 plasmid / 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: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.4 M NaF, 15% glycerol, 0.1 M Tris-HCl, 0.5 mM protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 9, 2009
Details: Collimating Mirror with two stripes (Si, Rh/Pt), Toroidal Focusing Mirror (Rh/P t)
RadiationMonochromator: SAGITALLY FOCUSED Si(111), KOHZU double crystal monochromator (DCM), featuring indirectly water-cooled first crystal and flat, long second crystal
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0 Å / Relative weight: 1
ReflectionResolution: 2.751→48.509 Å / Num. all: 9004 / Num. obs: 9004 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 82.68 Å2
Reflection shellResolution: 2.7505→2.9229 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementResolution: 2.751→48.509 Å / SU ML: 0.89 / σ(F): 2 / Phase error: 27.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2666 901 10.01 %
Rwork0.2485 --
obs0.2506 9004 99.99 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.046 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1305 Å2-0 Å2-0 Å2
2--6.1305 Å20 Å2
3----0.1844 Å2
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_d0.0121125
X-RAY DIFFRACTIONf_angle_d1.681526
X-RAY DIFFRACTIONf_dihedral_angle_d16.405412
X-RAY DIFFRACTIONf_chiral_restr0.107171
X-RAY DIFFRACTIONf_plane_restr0.008192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7505-2.92290.35881460.34961312X-RAY DIFFRACTION100
2.9229-3.14850.36581450.32741307X-RAY DIFFRACTION100
3.1485-3.46530.36211470.29321325X-RAY DIFFRACTION100
3.4653-3.96650.28341490.24151335X-RAY DIFFRACTION100
3.9665-4.99660.23321510.21591360X-RAY DIFFRACTION100
4.9966-48.51690.23841630.23791464X-RAY DIFFRACTION100

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