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- PDB-1u5f: Crystal Structure of the PH Domain of SKAP-Hom with 8 Vector-deri... -

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Basic information

Entry
Database: PDB / ID: 1u5f
TitleCrystal Structure of the PH Domain of SKAP-Hom with 8 Vector-derived N-terminal Residues
ComponentsSrc-associated adaptor protein
KeywordsSIGNALING PROTEIN / PH domain of SKAP-Hom / Artefactual dimerization induced by vector-derived sequence
Function / homology
Function and homology information


Signal regulatory protein family interactions / B cell activation / negative regulation of cell population proliferation / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SKAP family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...SKAP family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / 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 / SIRAS / Resolution: 1.9 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: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Thrombin cleavage results in a vector-derived linker peptide (RASVGSPG) before coding ...SEQUENCE Thrombin cleavage results in a vector-derived linker peptide (RASVGSPG) before coding sequence starting at residue 109.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Src-associated adaptor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1983
Polymers17,0061
Non-polymers1922
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Src-associated adaptor protein
hetero molecules

A: Src-associated adaptor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3966
Polymers34,0122
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area3640 Å2
ΔGint-84 kcal/mol
Surface area12760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.750, 78.750, 130.123
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 17006.016 Da / Num. of mol.: 1 / Fragment: PH Domain, residues 109-248 / Mutation: A110P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SCAP2 / Plasmid: pGEX-2TK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8BK74, UniProt: Q3UND0*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium Sulfate, Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.916 Å
DetectorDetector: CCD / Date: Jan 30, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 12365 / Num. obs: 11889 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2 / Num. unique all: 797 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.481 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 596 4.8 %RANDOM
Rwork0.22585 ---
obs0.22686 11768 98.99 %-
all-12365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.919 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0.49 Å20 Å2
2---0.98 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 10 8 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0221011
X-RAY DIFFRACTIONr_bond_other_d0.0040.02877
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9521358
X-RAY DIFFRACTIONr_angle_other_deg0.93332055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1570.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02222
X-RAY DIFFRACTIONr_nbd_refined0.2030.2153
X-RAY DIFFRACTIONr_nbd_other0.2620.2913
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0970.2598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2990.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8051.5592
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2212946
X-RAY DIFFRACTIONr_scbond_it4.2953419
X-RAY DIFFRACTIONr_scangle_it6.6734.5412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.226 39
Rwork0.27 841
obs-476

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