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- PDB-1ad5: SRC FAMILY KINASE HCK-AMP-PNP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ad5
TitleSRC FAMILY KINASE HCK-AMP-PNP COMPLEX
ComponentsHAEMATOPOETIC CELL KINASE HCK
KeywordsTYROSINE-PROTEIN KINASE / TRANSFERASE / SIGNAL TRANSDUCTION / SH2 / SH3 / PHOSPHORYLATION
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) / transport vesicle / lipopolysaccharide-mediated signaling pathway / negative regulation of inflammatory response to antigenic stimulus / extrinsic component of cytoplasmic side of plasma membrane / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / cell projection / caveola / 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 / cell surface receptor protein tyrosine kinase signaling pathway / 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 / signaling receptor binding / protein phosphorylation / focal adhesion / innate immune response / intracellular membrane-bounded organelle / 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 / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains ...Tyrosine-protein kinase HCK, SH2 domain / SH2 domain / SHC Adaptor Protein / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Tyrosine-protein kinase HCK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS/MAD / Resolution: 2.6 Å
AuthorsSicheri, F. / Moarefi, I. / Kuriyan, J.
CitationJournal: Nature / Year: 1997
Title: Crystal structure of the Src family tyrosine kinase Hck.
Authors: Sicheri, F. / Moarefi, I. / Kuriyan, J.
History
DepositionFeb 20, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAEMATOPOETIC CELL KINASE HCK
B: HAEMATOPOETIC CELL KINASE HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7818
Polymers100,6092
Non-polymers1,1736
Water0
1
A: HAEMATOPOETIC CELL KINASE HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8914
Polymers50,3041
Non-polymers5863
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HAEMATOPOETIC CELL KINASE HCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8914
Polymers50,3041
Non-polymers5863
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.767, 92.360, 178.290
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 HAEMATOPOETIC CELL KINASE HCK


Mass: 50304.348 Da / Num. of mol.: 2 / Fragment: SH3-SH2-KINASE-REGULATORY TAIL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Gene: HUMAN HCK / Cell line (production host): SF9 / Gene (production host): HUMAN HCK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08631, EC: 2.7.1.112
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion - hanging drop, seeding / pH: 6.5
Details: HANGING DROPS (1UL) OF 50MG/ML PROTEIN AND 10MM AMP-PNP WERE MIXED WITH EQUAL VOLUMES OF RESERVOIR BUFFER CONTAINING 150 MM CALCIUM ACETATE, 100MM CACODYLATE (PH 6.5), 7% PEG 8000 AND 16% ...Details: HANGING DROPS (1UL) OF 50MG/ML PROTEIN AND 10MM AMP-PNP WERE MIXED WITH EQUAL VOLUMES OF RESERVOIR BUFFER CONTAINING 150 MM CALCIUM ACETATE, 100MM CACODYLATE (PH 6.5), 7% PEG 8000 AND 16% V/V ETHYLENE GLYCOL. THE MIXED DROPS WERE THEN SEEDED AND STORED AT 19 DEGREES C., vapor diffusion - hanging drop and seeding, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
25 mMquercetin1dropcan be replaced by 2AMP-PMP
375 mMcalcium acetate1drop
450 mMcacodylate1drop
53.5 %(w/v)PEG80001drop
68 %(v/v)ethylene glycol1drop
7150 mMcalcium acetate1reservoir
8100 mMcacodylate1reservoir
97 %(w/v)PEG80001reservoir
1016 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→18 Å / Num. obs: 34027 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3 / Rsym value: 0.189 / % possible all: 92.8
Reflection
*PLUS
Num. measured all: 346924

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIRAS/MAD / Resolution: 2.6→18 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1493 5 %RANDOM
Rwork0.239 ---
obs0.239 29868 79.4 %-
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.6 Å20 Å20 Å2
2---23.7 Å20 Å2
3---22.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6972 0 66 0 7038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it3.4
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
RfactorNum. reflection% reflection
Rfree0.425 65 5 %
Rwork0.38 1374 -
obs--49.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.38

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