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- PDB-1u5g: Crystal Structure of the PH Domain of SKAP-Hom -

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Basic information

Entry
Database: PDB / ID: 1u5g
TitleCrystal Structure of the PH Domain of SKAP-Hom
ComponentsSrc-associated adaptor protein
KeywordsSIGNALING PROTEIN / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTang, Y. / Swanson, K. / Neel, B.G. / Eck, M.J.
CitationJournal: Mol.Cell / Year: 2008
Title: The Skap-hom dimerization and PH domains comprise a 3'-phosphoinositide-gated molecular switch.
Authors: Swanson, K.D. / Tang, Y. / Ceccarelli, D.F. / Poy, F. / Sliwa, J.P. / 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 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 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
C: Src-associated adaptor protein
D: Src-associated adaptor protein


Theoretical massNumber of molelcules
Total (without water)56,8334
Polymers56,8334
Non-polymers00
Water3,837213
1
A: Src-associated adaptor protein


Theoretical massNumber of molelcules
Total (without water)14,2081
Polymers14,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Src-associated adaptor protein


Theoretical massNumber of molelcules
Total (without water)14,2081
Polymers14,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Src-associated adaptor protein


Theoretical massNumber of molelcules
Total (without water)14,2081
Polymers14,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Src-associated adaptor protein


Theoretical massNumber of molelcules
Total (without water)14,2081
Polymers14,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.613, 65.695, 143.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14208.134 Da / Num. of mol.: 4 / Fragment: PH Domain, residues 101-222 / Mutation: S101G, D102S
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: Q8BK74, UniProt: Q3UND0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 19, 2003 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 33609 / Num. obs: 31477 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.3
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2178 / % possible all: 97.9

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Crystal Structure of the PH Domain of SKAP-Hom with Vector-derived N-terminal Linker Peptide, PDB entry 1U5F.

1u5f


Resolution: 2.1→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1691 -RANDOM
Rwork0.213 ---
all0.216 33609 --
obs0.216 31477 99.4 %-
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 0 213 4091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.034
X-RAY DIFFRACTIONr_angle_refined_deg2.337
LS refinement shellResolution: 2.1→2.154 Å
RfactorNum. reflection% reflection
Rfree0.308 127 -
Rwork0.213 --
obs-2295 84.7 %

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