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- PDB-4hzs: Crystal structure of Ack1 kinase domain with C-terminal SH3 domain -

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Basic information

Entry
Database: PDB / ID: 4hzs
TitleCrystal structure of Ack1 kinase domain with C-terminal SH3 domain
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE / inactive state / allostery / dimerization / oligomerization / negative regulation / activation / phosphotransfer
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / WW domain binding / phosphorylation ...regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / WW domain binding / phosphorylation / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / non-specific protein-tyrosine kinase / adherens junction / non-membrane spanning protein tyrosine kinase activity / cytoplasmic vesicle membrane / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / SAM domain-like / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / Variant SH3 domain ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / SAM domain-like / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / Variant SH3 domain / Src homology 3 domains / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 Alpha / Alpha Beta
Similarity search - Domain/homology
Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsGajiwala, K.S.
CitationJournal: Plos One / Year: 2013
Title: Ack1: activation and regulation by allostery.
Authors: Gajiwala, K.S. / Maegley, K. / Ferre, R. / He, Y.A. / Yu, X.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activated CDC42 kinase 1
B: Activated CDC42 kinase 1
C: Activated CDC42 kinase 1
D: Activated CDC42 kinase 1


Theoretical massNumber of molelcules
Total (without water)155,4464
Polymers155,4464
Non-polymers00
Water00
1
A: Activated CDC42 kinase 1


Theoretical massNumber of molelcules
Total (without water)38,8621
Polymers38,8621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Activated CDC42 kinase 1


Theoretical massNumber of molelcules
Total (without water)38,8621
Polymers38,8621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Activated CDC42 kinase 1


Theoretical massNumber of molelcules
Total (without water)38,8621
Polymers38,8621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Activated CDC42 kinase 1


Theoretical massNumber of molelcules
Total (without water)38,8621
Polymers38,8621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.463, 145.463, 103.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Activated CDC42 kinase 1 / Ack1 / ACK-1 / Tyrosine kinase non-receptor protein 2


Mass: 38861.527 Da / Num. of mol.: 4
Fragment: protein kinase and SH3 domains (UNP residues 115-453)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNK2, ACK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase

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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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.6, 22-24% PEG3350, 10-20 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2010 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→73.04 Å / Num. all: 34878 / Num. obs: 34878 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.187 / Net I/σ(I): 9.9
Reflection shellResolution: 3.23→3.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2 / Num. unique all: 4895 / % possible all: 96.7

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Processing

Software
NameClassification
JDirectordata collection
CNXrefinement
autoPROCdata scaling
SCALAdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→73.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2252595.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1717 4.9 %RANDOM
Rwork0.246 ---
all0.247 34753 --
obs0.247 34753 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.8734 Å2 / ksol: 0.305827 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20 Å20 Å2
2--3.69 Å20 Å2
3----7.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3.23→73.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10196 0 0 0 10196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.872.5
Refine LS restraints NCSWeight Biso : 2 / Weight position: 300
LS refinement shellResolution: 3.23→3.43 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 259 4.6 %
Rwork0.326 5388 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paraprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paradna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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