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- PDB-1u5d: Crystal Structure of the PH domain of SKAP55 -

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Basic information

Entry
Database: PDB / ID: 1u5d
TitleCrystal Structure of the PH domain of SKAP55
ComponentsSrc Kinase-associated Phosphoprotein of 55 kDa
KeywordsSIGNALING PROTEIN / PH Domain
Function / homology
Function and homology information


positive regulation of leukocyte cell-cell adhesion / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of adaptive immune response / positive regulation of integrin activation / positive regulation of heterotypic cell-cell adhesion / positive regulation of cell-matrix adhesion / T cell receptor complex / immunological synapse / plasma membrane raft / SH2 domain binding ...positive regulation of leukocyte cell-cell adhesion / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of adaptive immune response / positive regulation of integrin activation / positive regulation of heterotypic cell-cell adhesion / positive regulation of cell-matrix adhesion / T cell receptor complex / immunological synapse / plasma membrane raft / SH2 domain binding / protein localization to plasma membrane / SH3 domain binding / cell-cell junction / T cell receptor signaling pathway / protein phosphatase binding / adaptive immune response / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Src kinase-associated phosphoprotein 1, SH3 domain / SKAP family / Variant SH3 domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains ...Src kinase-associated phosphoprotein 1, SH3 domain / SKAP family / Variant SH3 domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology 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 1 / Src kinase-associated phosphoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / 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 1.4Aug 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 Kinase-associated Phosphoprotein of 55 kDa
B: Src Kinase-associated Phosphoprotein of 55 kDa
C: Src Kinase-associated Phosphoprotein of 55 kDa
D: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,56611
Polymers50,8944
Non-polymers6727
Water7,692427
1
A: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9163
Polymers12,7231
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8192
Polymers12,7231
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9163
Polymers12,7231
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9163
Polymers12,7231
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

B: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

C: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

D: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,56611
Polymers50,8944
Non-polymers6727
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_444x-1,y-1,z-11
crystal symmetry operation1_454x-1,y,z-11
Buried area5980 Å2
ΔGint-132 kcal/mol
Surface area23050 Å2
MethodPISA
6
A: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

B: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

C: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

D: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,56611
Polymers50,8944
Non-polymers6727
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_636-x+1,y-3/2,-z+11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area6770 Å2
ΔGint-127 kcal/mol
Surface area22260 Å2
MethodPISA
7
A: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

B: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7355
Polymers25,4472
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2640 Å2
ΔGint-59 kcal/mol
Surface area11800 Å2
MethodPISA
8
C: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

D: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8316
Polymers25,4472
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2680 Å2
ΔGint-61 kcal/mol
Surface area11910 Å2
MethodPISA
9
C: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules

B: Src Kinase-associated Phosphoprotein of 55 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7355
Polymers25,4472
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_566x,y+1,z+11
Buried area1240 Å2
ΔGint-53 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.068, 33.352, 105.382
Angle α, β, γ (deg.)90.00, 110.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Src Kinase-associated Phosphoprotein of 55 kDa / SKAP55


Mass: 12723.417 Da / Num. of mol.: 4 / Fragment: PH Domain (residues 106-213) / Mutation: D106G, N107S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSSKAP55 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O15268, UniProt: Q86WV1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.5 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Ammonium Sulfate, Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.978 Å
DetectorDetector: CCD / Date: Dec 1, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. all: 45815 / Num. obs: 45007 / % possible obs: 83.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 4 / Num. unique all: 2179 / % possible all: 40.3

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Processing

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

1u5g


Resolution: 1.7→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
Rfree0.185 2334 -RANDOM
Rwork0.168 ---
all0.168 45815 --
obs0.168 45007 84.75 %-
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 35 427 4040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.019
X-RAY DIFFRACTIONr_angle_refined_deg1.8
LS refinement shellResolution: 1.7→1.74 Å
RfactorNum. reflection
Rfree0.259 65
Rwork0.206 -
obs-1513

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