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- PDB-5jn0: CRK-II SH2 domain -

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Basic information

Entry
Database: PDB / ID: 5jn0
TitleCRK-II SH2 domain
ComponentsCRK-II SH2 domain
KeywordsPROTEIN BINDING / SH2 domain
Function / homology
Function and homology information


PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / Downstream signal transduction ...PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / Downstream signal transduction / postsynaptic specialization assembly / regulation of leukocyte migration / protein phosphorylated amino acid binding / regulation of T cell migration / p130Cas linkage to MAPK signaling for integrins / regulation of dendrite development / response to peptide / positive regulation of skeletal muscle acetylcholine-gated channel clustering / response to yeast / Regulation of signaling by CBL / negative regulation of wound healing / Regulation of actin dynamics for phagocytic cup formation / reelin-mediated signaling pathway / negative regulation of cell motility / VEGFA-VEGFR2 Pathway / negative regulation of natural killer cell mediated cytotoxicity / protein localization to membrane / regulation of GTPase activity / cellular response to insulin-like growth factor stimulus / enzyme-linked receptor protein signaling pathway / positive regulation of smooth muscle cell migration / establishment of cell polarity / dendrite development / regulation of cell adhesion mediated by integrin / positive regulation of Rac protein signal transduction / ephrin receptor signaling pathway / cellular response to transforming growth factor beta stimulus / cytoskeletal protein binding / signaling adaptor activity / insulin-like growth factor receptor binding / ephrin receptor binding / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / cellular response to nitric oxide / SH2 domain binding / protein tyrosine kinase binding / hippocampus development / cell chemotaxis / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / neuron migration / cellular response to nerve growth factor stimulus / neuromuscular junction / response to hydrogen peroxide / lipid metabolic process / cerebral cortex development / SH3 domain binding / actin cytoskeleton / signaling receptor complex adaptor activity / regulation of cell shape / actin cytoskeleton organization / scaffold protein binding / cell population proliferation / ubiquitin protein ligase binding / protein-containing complex / membrane / plasma membrane / cytoplasm
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Adapter molecule crk
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.677 Å
AuthorsCho, J.-H.
CitationJournal: To Be Published
Title: CRK-II SH2 domain
Authors: Cho, J.-H.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRK-II SH2 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3993
Polymers11,3291
Non-polymers712
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.082, 86.082, 33.847
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-466-

HOH

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Components

#1: Protein CRK-II SH2 domain


Mass: 11328.528 Da / Num. of mol.: 1 / Fragment: UNP residues 6-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q64010
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES pH 6.5, 12% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.67→30.819 Å / Num. obs: 10693 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.028 / Rrim(I) all: 0.056 / Χ2: 1 / Net I/av σ(I): 30.751 / Net I/σ(I): 14.8 / Num. measured all: 40731
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.67-1.71.80.173860.9270.1430.2220.52269.9
1.7-1.733.70.185160.9660.1070.210.594100
1.73-1.763.80.155730.9750.0880.1750.543100
1.76-1.83.80.1345170.9770.0790.1560.564100
1.8-1.843.80.1185370.9840.070.1370.565100
1.84-1.883.90.1015860.9880.060.1180.571100
1.88-1.933.90.0865150.9920.050.10.633100
1.93-1.983.90.0745500.9940.0440.0860.646100
1.98-2.043.90.0615530.9960.0360.0710.698100
2.04-2.13.90.0545440.9970.0320.0630.697100
2.1-2.183.90.0485150.9970.0280.0550.726100
2.18-2.273.90.0665610.8550.040.0771.659100
2.27-2.373.90.0495370.9960.0290.0570.927100
2.37-2.493.90.0465460.9970.0270.0530.957100
2.49-2.653.90.0435450.9970.0250.050.908100
2.65-2.863.90.0395430.9970.0230.0461.058100
2.86-3.143.90.0375320.9980.0210.0431.212100
3.14-3.640.0345520.9980.020.041.495100
3.6-4.533.90.045440.9970.0230.0462.146100
4.53-5040.0455410.9940.0260.0522.32799.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 1.677→30.819 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 18.35
RfactorNum. reflection% reflection
Rfree0.2098 513 4.8 %
Rwork0.1695 --
obs0.1713 10693 99.65 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 32.636 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 58.13 Å2 / Biso mean: 16.92 Å2 / Biso min: 3.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.4536 Å20 Å20 Å2
2---1.4536 Å20 Å2
3---2.9071 Å2
Refinement stepCycle: final / Resolution: 1.677→30.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 0 2 168 953
Biso mean--36.38 30.09 -
Num. residues----96
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002831
X-RAY DIFFRACTIONf_angle_d0.7661129
X-RAY DIFFRACTIONf_chiral_restr0.054121
X-RAY DIFFRACTIONf_plane_restr0.003148
X-RAY DIFFRACTIONf_dihedral_angle_d11.373308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.677-1.84560.20811050.19222530263599
1.8456-2.11260.21351440.159725592703100
2.1126-2.66150.22871340.168225402674100
2.6615-30.82440.19721300.168525512681100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.40941.26960.37092.58170.5892.2037-0.09320.21810.05-0.11820.0834-0.0702-0.05280.01030.00930.0521-0.0040.00950.0690.01020.0341.7219-14.210429.7888
21.7274-0.05950.15162.5777-0.15391.8687-0.0249-0.17430.02160.1755-0.0062-0.03890.0041-0.00790.01820.0514-0.00570.00250.08960.00430.0322-2.6055-17.558439.405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:39)A6 - 39
2X-RAY DIFFRACTION2chain 'A' and (resseq 40:104)A40 - 104

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