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- PDB-1u54: Crystal Structures of the Phosphorylated and Unphosphorylated Kin... -

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Basic information

Entry
Database: PDB / ID: 1u54
TitleCrystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the CDC42-associated Tyrosine Kinase ACK1 bound to AMP-PCP
Components(Activated CDC42 kinase 1) x 2
KeywordsTRANSFERASE / Tyrosine Kinase
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / small GTPase-mediated signal transduction / epidermal growth factor receptor binding / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity ...regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / small GTPase-mediated signal transduction / epidermal growth factor receptor binding / 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 / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLougheed, J.C. / Chen, R.H. / Mak, P. / Stout, T.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the Cdc42-associated Tyrosine Kinase ACK1.
Authors: Lougheed, J.C. / Chen, R.H. / Mak, P. / Stout, T.J.
History
DepositionJul 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)67,3048
Polymers66,1962
Non-polymers1,1086
Water18010
1
A: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6924
Polymers33,1381
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6124
Polymers33,0581
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.384, 42.332, 70.848
Angle α, β, γ (deg.)90.00, 96.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Activated CDC42 kinase 1 / ACK-1


Mass: 33138.023 Da / Num. of mol.: 1 / Fragment: Kinase Domain
Source method: isolated from a genetically manipulated source
Details: phosphorylated at residue 284 / Source: (gene. exp.) Homo sapiens (human) / Gene: ACK1 / Cell line (production host): Sf-9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q07912, EC: 2.7.1.112
#2: Protein Activated CDC42 kinase 1 / ACK-1


Mass: 33058.047 Da / Num. of mol.: 1 / Fragment: Kinase Domain
Source method: isolated from a genetically manipulated source
Details: unphosphorylated at residue 284 / Source: (gene. exp.) Homo sapiens (human) / Gene: ACK1 / Cell line (production host): Sf-9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q07912, EC: 2.7.1.112
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.3 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 291 K / pH: 8.5
Details: PEG 4000, lithium sulfate, magnesium chloride, sodium chloride, AMP-PCP, Tris, TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.954
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.8→38.71 Å / Num. obs: 14697 / % possible obs: 98.3 % / Redundancy: 3.6 % / Rsym value: 0.058 / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.64 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.319 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U46

1u46


Resolution: 2.8→38.71 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.842 / SU B: 19.96 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.51
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS REFINEMENT WAS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.322 684 4.7 %RANDOM
Rwork0.222 ---
obs0.226 14697 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å21.56 Å2
2--2.98 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 66 10 4293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214379
X-RAY DIFFRACTIONr_bond_other_d0.0020.024008
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.9775935
X-RAY DIFFRACTIONr_angle_other_deg0.91239292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3435517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024744
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02910
X-RAY DIFFRACTIONr_nbd_refined0.2520.2968
X-RAY DIFFRACTIONr_nbd_other0.2310.24650
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.22671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.52604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89624188
X-RAY DIFFRACTIONr_scbond_it1.5131775
X-RAY DIFFRACTIONr_scangle_it2.294.51747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 40
Rwork0.239 1010
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.8823-1.12091.89994.89580.36395.2570.1521-0.74460.64330.06560.2137-0.9306-0.15060.3833-0.36580.2199-0.05740.07230.3688-0.06330.656443.14419.35454.437
28.8949-0.9118-3.23583.88551.13265.0280.020.742-0.8754-0.3559-0.25740.57270.1127-0.12790.23740.25610.0575-0.07990.0209-0.07490.430419.55313.30449.929
38.8796-1.12851.39133.1795-0.21626.69110.0494-0.0769-0.24070.28410.0597-0.31020.22140.1714-0.10910.19490.008-0.01580.3768-0.03890.400126.90628.16393.012
43.5665-0.05120.18242.58041.58785.88740.0766-0.3748-0.06880.1874-0.1848-0.0841-0.0726-1.36550.10820.11950.08650.00740.69130.10340.27855.79326.54479.813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA115 - 2069 - 100
2X-RAY DIFFRACTION2AA207 - 390101 - 284
3X-RAY DIFFRACTION3BB117 - 20611 - 100
4X-RAY DIFFRACTION4BB207 - 388101 - 282

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