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- PDB-1bu1: SRC FAMILY KINASE HCK SH3 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1bu1
TitleSRC FAMILY KINASE HCK SH3 DOMAIN
ComponentsPROTEIN (HEMOPOIETIC CELL KINASE)
KeywordsTRANSFERASE / TYROSINE-PROTEIN KINASE / SIGNAL TRANSDUCTION / SH3
Function / homology
Function and homology information


leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization ...leukocyte degranulation / respiratory burst after phagocytosis / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / regulation of podosome assembly / regulation of phagocytosis / FLT3 signaling through SRC family kinases / Nef and signal transduction / regulation of DNA-binding transcription factor activity / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / FCGR activation / localization / type II interferon-mediated signaling pathway / Signaling by CSF3 (G-CSF) / lipopolysaccharide-mediated signaling pathway / transport vesicle / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / caveola / cell projection / integrin-mediated signaling pathway / Regulation of signaling by CBL / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / regulation of inflammatory response / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / lysosome / cytoskeleton / cell adhesion / intracellular signal transduction / inflammatory response / protein phosphorylation / intracellular membrane-bounded organelle / innate immune response / focal adhesion / signaling receptor binding / lipid binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase HCK, SH2 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...Tyrosine-protein kinase HCK, SH2 domain / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein kinase HCK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsArold, S. / Franken, P. / Dumas, C.
CitationJournal: Biochemistry / Year: 1998
Title: RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef.
Authors: Arold, S. / O'Brien, R. / Franken, P. / Strub, M.P. / Hoh, F. / Dumas, C. / Ladbury, J.E.
History
DepositionSep 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Jun 30, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.6Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PROTEIN (HEMOPOIETIC CELL KINASE)
B: PROTEIN (HEMOPOIETIC CELL KINASE)
C: PROTEIN (HEMOPOIETIC CELL KINASE)
D: PROTEIN (HEMOPOIETIC CELL KINASE)
E: PROTEIN (HEMOPOIETIC CELL KINASE)
F: PROTEIN (HEMOPOIETIC CELL KINASE)


Theoretical massNumber of molelcules
Total (without water)39,8136
Polymers39,8136
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.500, 106.150, 78.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.865926, -0.35656, -0.350766), (-0.318783, -0.933831, 0.162286), (-0.385421, -0.028709, -0.922294)19.916, 59.847, 39.696
3given(0.34811, 0.026107, -0.93709), (-0.079585, -0.99518, -0.05729), (-0.93407, 0.094522, -0.344354)24.557, 35.9, 29.955
4given(-0.740098, 0.154611, -0.654485), (-0.235476, -0.971181, 0.036854), (-0.629925, 0.181391, 0.755176)56.38, 9.535, -2.428
5given(0.63133, -0.14705, 0.761445), (0.303052, 0.950567, -0.067693), (-0.71385, 0.273494, 0.644685)17.671, 16.976, 9.116
6given(0.238708, -0.210432, -0.948017), (-0.199078, -0.966109, 0.164321), (-0.950466, 0.149505, -0.27251)54.839, 35.953, 64.184

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Components

#1: Protein
PROTEIN (HEMOPOIETIC CELL KINASE) / EC 2.7.1.112 TRANSFERASE


Mass: 6635.428 Da / Num. of mol.: 6 / Fragment: SH3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 (DE3) / Gene: HUMAN HCK / Species (production host): Escherichia coli / Gene (production host): HUMAN HCK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P08631, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.3
Details: HANGING DROPS (2UL) OF 4.3MG/ML PROTEIN WERE MIXED WITH EQUAL VOLUMES OF RESERVOIR BUFFER CONTAINING 3.7 M SODIUM FORMATE, 2% PEG 3000, 100 MM BICINE (PH 9.3). THE MIXED DROPS WERE STORED AT ...Details: HANGING DROPS (2UL) OF 4.3MG/ML PROTEIN WERE MIXED WITH EQUAL VOLUMES OF RESERVOIR BUFFER CONTAINING 3.7 M SODIUM FORMATE, 2% PEG 3000, 100 MM BICINE (PH 9.3). THE MIXED DROPS WERE STORED AT 21 DEGREES, vapor diffusion - hanging drop, temperature 294K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.3 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mM1dropNaCl
41 mMEGTA1drop
5100 mMBicine1reservoir
63.7 Msodium formate1reservoir
72 %PEG30001reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.074
DetectorType: PRINCETON / THOMSON / Detector: CCD / Date: Nov 15, 1996 / Details: TWO BENT MIRRORS
RadiationMonochromator: TWO SILICON CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 2.6→34 Å / Num. obs: 13043 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 35
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.189 / Rsym value: 0.189 / % possible all: 62.1
Reflection shell
*PLUS
Lowest resolution: 2.72 Å / % possible obs: 62 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HCK

2hck


Resolution: 2.6→34 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 588 4.5 %RANDOM
Rwork0.233 ---
obs0.233 13043 93.1 %-
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.1 Å20 Å20 Å2
2---13.1 Å20 Å2
3---10.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 0 70 2857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.27
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.81
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.148
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 13
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 34 Å / σ(F): 0 / % reflection Rfree: 4.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.81
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.148
LS refinement shell
*PLUS
Highest resolution: 2.6 Å

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