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- PDB-2bzx: Atomic model of CrkL-SH3C monomer -

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Basic information

Entry
Database: PDB / ID: 2bzx
TitleAtomic model of CrkL-SH3C monomer
ComponentsCRK-LIKE PROTEIN
KeywordsSH3 DOMAIN / CRKL / SH3C / MONOMER / NATIVE / NUCLEAR EXPORT
Function / homology
Function and homology information


positive regulation of glial cell migration / helper T cell diapedesis / cerebellar neuron development / chordate pharynx development / extrinsic component of postsynaptic membrane / postsynaptic specialization assembly / urogenital system development / parathyroid gland development / regulation of T cell migration / regulation of dendrite development ...positive regulation of glial cell migration / helper T cell diapedesis / cerebellar neuron development / chordate pharynx development / extrinsic component of postsynaptic membrane / postsynaptic specialization assembly / urogenital system development / parathyroid gland development / regulation of T cell migration / regulation of dendrite development / endothelin receptor signaling pathway / positive regulation of skeletal muscle acetylcholine-gated channel clustering / cranial skeletal system development / reelin-mediated signaling pathway / B cell apoptotic process / MET receptor recycling / cellular response to interleukin-7 / MET activates RAP1 and RAC1 / acetylcholine receptor signaling pathway / anterior/posterior pattern specification / Frs2-mediated activation / enzyme-linked receptor protein signaling pathway / negative regulation of SMAD protein signal transduction / establishment of cell polarity / blood vessel development / regulation of cell adhesion mediated by integrin / dendrite development / positive regulation of Rac protein signal transduction / outflow tract morphogenesis / single fertilization / fibroblast growth factor receptor signaling pathway / retinoic acid receptor signaling pathway / Erythropoietin activates RAS / cellular response to transforming growth factor beta stimulus / JNK cascade / signaling adaptor activity / positive regulation of substrate adhesion-dependent cell spreading / phosphotyrosine residue binding / Downstream signal transduction / thymus development / hippocampus development / cell chemotaxis / Regulation of signaling by CBL / regulation of cell growth / neuromuscular junction / cerebral cortex development / receptor tyrosine kinase binding / lipid metabolic process / male gonad development / neuron migration / cellular response to xenobiotic stimulus / cell migration / T cell receptor signaling pathway / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / cadherin binding / negative regulation of gene expression / positive regulation of cell population proliferation / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...CRK, N-terminal SH3 domain / CRK, C-terminal SH3 domain / : / Variant SH3 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHarkiolaki, M. / Gilbert, R.J. / Jones, E.Y. / Feller, S.M.
CitationJournal: Structure / Year: 2006
Title: The C-Terminal SH3 Domain of Crkl as a Dynamic Dimerization Module Transiently Exposing a Nuclear Export Signal.
Authors: Harkiolaki, M. / Gilbert, R.J. / Jones, E.Y. / Feller, S.M.
History
DepositionAug 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRK-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)7,5521
Polymers7,5521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.285, 53.285, 51.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CRK-LIKE PROTEIN


Mass: 7551.613 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOPP1 / References: UniProt: P46109
Compound detailsMAY MEDIATE THE TRANSDUCTION OF INTRACELLULAR SIGNALS.
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: 2.75 Å3/Da / Density % sol: 54.91 %
Crystal growpH: 6.5
Details: 1.7M AMMONIUM SULPHATE, 25.5% W/V PEG 8000, 0.085M SODIUM CACODYLATE PH6.5, 15% V/V GLYCEROL, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7712
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 8, 2003 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 2035 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 38.8 % / Biso Wilson estimate: 87 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 34.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 26.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UEC

1uec


Resolution: 2.8→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R-VALUE / σ(F): 1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3743 101 5 %RANDOM
Rwork0.3173 ---
obs0.3173 2015 99.9 %-
Solvent computationSolvent model: CNS BULK SOLVENT CORRECTION / Bsol: 60 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 73.3 Å2
Baniso -1Baniso -2Baniso -3
1--11.813 Å20 Å20 Å2
2---11.813 Å20 Å2
3---23.626 Å2
Refine analyzeLuzzati coordinate error obs: 0.506 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 0 0 474
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011707
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_deg1.9815
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_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.393
X-RAY DIFFRACTIONc_mcangle_it5.594
X-RAY DIFFRACTIONc_scbond_it5.284
X-RAY DIFFRACTIONc_scangle_it7.285
LS refinement shellResolution: 2.8→2.93 Å / Rfactor Rfree error: 0.135 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4049 9 3.9 %
Rwork0.3728 222 -
obs--100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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