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- PDB-3cio: The kinase domain of Escherichia coli tyrosine kinase ETK -

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Basic information

Entry
Database: PDB / ID: 3cio
TitleThe kinase domain of Escherichia coli tyrosine kinase ETK
ComponentsTyrosine-protein kinase etk
KeywordsSIGNALING PROTEIN / TRANSFERASE / ETK / WZC / ESCHERICHIA COLI TYROSINE KINASE DOMAIN / Inner membrane / Membrane / Phosphoprotein / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Protein-tyrosine kinases / extracellular polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / peptidyl-tyrosine autophosphorylation / protein tyrosine kinase activity / membrane => GO:0016020 / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Tyrosine kinase, G-rich domain / G-rich domain on putative tyrosine kinase / Exopolysaccharide synthesis protein / Polysaccharide chain length determinant N-terminal domain / Chain length determinant protein / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase etk
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLee, D.C. / Zheng, J. / Jia, Z.
CitationJournal: Embo J. / Year: 2008
Title: Structure of Escherichia coli tyrosine kinase Etk reveals a novel activation mechanism.
Authors: Lee, D.C. / Zheng, J. / She, Y.M. / Jia, Z.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase etk
D: Tyrosine-protein kinase etk
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8445
Polymers66,7372
Non-polymers1063
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.514, 51.731, 120.519
Angle α, β, γ (deg.)90.00, 114.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine-protein kinase etk / ETK


Mass: 33368.633 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN (UNP residues 452-726)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: etk, yccC / Plasmid: PCA24N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DL41
References: UniProt: P38134, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.14M AMMONIUM SULFATE, 17% PEG 8000, 0.014M EDTA, 0.086M BIS-TRIS. ADDITIVE: 1M SODIUM BROMIDE, OR 40% ACETONITRILE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 3, 2006
RadiationMonochromator: BENT TRIANGULAR ASYMMETRIC CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→29.93 Å / Num. obs: 23004 / % possible obs: 59.7 % / Observed criterion σ(I): 32.6 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Rsym value: 0.064 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.407 / % possible all: 61.8

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.93 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 776 3.4 %5%
Rwork0.196 ---
obs0.196 15757 69.2 %-
Solvent computationBsol: 58.74 Å2
Displacement parametersBiso mean: 67.64 Å2
Baniso -1Baniso -2Baniso -3
1-17.989 Å20 Å2-14.454 Å2
2--12.023 Å20 Å2
3----30.011 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 3 114 4062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
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_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.7651.5
X-RAY DIFFRACTIONc_mcangle_it5.5712
X-RAY DIFFRACTIONc_scbond_it5.6022
X-RAY DIFFRACTIONc_scangle_it7.6052.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION4PTR_XPLOR_PAR.TXT
X-RAY DIFFRACTION5SO4_XPLOR_PAR.TXT

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