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- PDB-1rpy: CRYSTAL STRUCTURE OF THE DIMERIC SH2 DOMAIN OF APS -

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Basic information

Entry
Database: PDB / ID: 1rpy
TitleCRYSTAL STRUCTURE OF THE DIMERIC SH2 DOMAIN OF APS
Componentsadaptor protein APS
KeywordsSIGNALING PROTEIN / ADAPTER PROTEIN / SH2 DOMAIN
Function / homology
Function and homology information


Regulation of KIT signaling / Factors involved in megakaryocyte development and platelet production / antigen receptor-mediated signaling pathway / regulation of Ras protein signal transduction / B-1 B cell homeostasis / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of metabolic process / regulation of immune response / brown fat cell differentiation / stress fiber ...Regulation of KIT signaling / Factors involved in megakaryocyte development and platelet production / antigen receptor-mediated signaling pathway / regulation of Ras protein signal transduction / B-1 B cell homeostasis / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of metabolic process / regulation of immune response / brown fat cell differentiation / stress fiber / ruffle / signaling adaptor activity / SH2 domain binding / actin filament / B cell receptor signaling pathway / cytokine-mediated signaling pathway / insulin receptor signaling pathway / nervous system development / actin cytoskeleton organization / intracellular signal transduction / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SH2B2, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / SH2 domain / SHC Adaptor Protein / PH domain / PH domain profile. / Pleckstrin homology domain. ...SH2B2, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / SH2 domain / SHC Adaptor Protein / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SH2B adapter protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsHu, J. / Liu, J. / Ghirlando, R. / Saltiel, A.R. / Hubbard, S.R.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural basis for recruitment of the adaptor protein APS to the activated insulin receptor.
Authors: Hu, J. / Liu, J. / Ghirlando, R. / Saltiel, A.R. / Hubbard, S.R.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: adaptor protein APS
B: adaptor protein APS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0694
Polymers25,8772
Non-polymers1922
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-63 kcal/mol
Surface area9580 Å2
MethodPISA
2
A: adaptor protein APS
B: adaptor protein APS
hetero molecules

A: adaptor protein APS
B: adaptor protein APS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1398
Polymers51,7544
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7880 Å2
ΔGint-141 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.378, 78.378, 67.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein adaptor protein APS


Mass: 12938.573 Da / Num. of mol.: 2 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z200
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5 / Details: Ammonium sulfate/tris, pH 7.5, pH 7.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
21.4 Mammonium sulfate1reservoir
3100 MTris1reservoirpH7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9789
DetectorDate: Jul 18, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 10560 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.05 / Net I/σ(I): 19.8
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.199 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 19797 / % possible obs: 96.4 % / Num. measured all: 75619 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.183

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNSrefinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.27 542 5 %RANDOM
Rwork0.228 ---
obs0.228 10288 94.1 %-
all-10934 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4 Å2-2.4 Å20 Å2
2---5.4 Å20 Å2
3---10.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 10 30 1400
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.72.5
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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