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- PDB-4hzr: Crystal structure of Ack1 kinase domain -

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Basic information

Entry
Database: PDB / ID: 4hzr
TitleCrystal structure of Ack1 kinase domain
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE / active state / phosphotransfer
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / regulation of keratinocyte differentiation / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / WW domain binding / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / negative regulation of epidermal growth factor receptor signaling pathway ...regulation of clathrin-dependent endocytosis / regulation of keratinocyte differentiation / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / WW domain binding / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / negative regulation of epidermal growth factor receptor signaling pathway / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / adherens junction / non-specific protein-tyrosine kinase / 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 / phosphorylation / 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 / cytoplasm / cytosol
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / 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 ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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: 1.31 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 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5217
Polymers63,1692
Non-polymers3525
Water8,935496
1
A: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7433
Polymers31,5841
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7784
Polymers31,5841
Non-polymers1943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.057, 42.340, 92.590
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31584.426 Da / Num. of mol.: 2 / Fragment: protein kinase domain (UNP residues 115-389)
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M bicine, pH 9.0, 12-15% PEG400, 25 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2009 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. all: 130862 / Num. obs: 127861 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.2
Reflection shellResolution: 1.31→1.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.3 / Num. unique all: 13007 / % possible all: 93.6

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Processing

Software
NameClassification
MAR345dtbdata collection
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→38.43 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 150745.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 5936 4.9 %RANDOM
Rwork0.196 ---
obs0.197 122057 92.9 %-
all-128723 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6504 Å2 / ksol: 0.385825 e/Å3
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-1.6 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.31→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 19 496 4698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
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_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 1.31→1.39 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 868 5 %
Rwork0.248 16579 -
obs--80.2 %
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
X-RAY DIFFRACTION5edo.paramedo.top

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