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- PDB-1u5e: Crystal Structure of a N-terminal Fragment of SKAP-Hom Containing... -

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Basic information

Entry
Database: PDB / ID: 1u5e
TitleCrystal Structure of a N-terminal Fragment of SKAP-Hom Containing Both the Helical Dimerization Domain and the PH Domain
ComponentsSrc-associated adaptor protein
KeywordsSIGNALING PROTEIN / Novel Dimerization Domain / PH Domain
Function / homology
Function and homology information


Signal regulatory protein family interactions / B cell activation / negative regulation of cell population proliferation / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / SKAP family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / SKAP family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Helix non-globular / Special / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Src kinase-associated phosphoprotein 2 / Src kinase-associated phosphoprotein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTang, Y. / Swanson, K.D. / Neel, B.G. / Eck, M.J.
CitationJournal: To be Published
Title: Structural Basis for the Dimerization and Phosphoinositide Specificity of the Src Kinase-associated Phosphoproteins SKAP55 and SKAP-Hom
Authors: Tang, Y. / Swanson, K.D. / Neel, B.G. / Eck, M.J.
History
DepositionJul 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Src-associated adaptor protein
B: Src-associated adaptor protein


Theoretical massNumber of molelcules
Total (without water)48,3442
Polymers48,3442
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-20 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.205, 56.742, 89.115
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiological dimer

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Components

#1: Protein Src-associated adaptor protein / SKAP55 homologue


Mass: 24171.980 Da / Num. of mol.: 2 / Fragment: N-terminal Fragment, residues 12-222 / Mutation: P12G, L13S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SCAP2 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z2K4, UniProt: Q3UND0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 4000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorDetector: CCD / Date: Oct 6, 2003 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. all: 16284 / Num. obs: 15738 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.9
Reflection shellResolution: 2.6→2.66 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / Num. unique all: 1075 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The PH Domain of SKAP-Hom, PDB entry 1u5g

1u5g


Resolution: 2.6→35 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.216 819 -RANDOM
Rwork0.179 ---
all0.181 16284 --
obs0.181 15738 98.7 %-
Displacement parametersBiso mean: 60 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 0 23 2807
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.05
X-RAY DIFFRACTIONr_angle_refined_deg3.2
LS refinement shellResolution: 2.6→2.667 Å
RfactorNum. reflection% reflection
Rfree0.341 53 -
Rwork0.259 --
obs-1117 97.4 %

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