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- PDB-8e4t: Crystal structure of the kinase domain of RTKC8 from the choanofl... -

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Basic information

Entry
Database: PDB / ID: 8e4t
TitleCrystal structure of the kinase domain of RTKC8 from the choanoflagellate Monosiga brevicollis
ComponentsRTKC8 Kinase domain
KeywordsTRANSFERASE / Receptor Tyrosine Kinase Staurosporine
Function / homology
Function and homology information


positive regulation of kinase activity / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / receptor complex / protein phosphorylation / ATP binding / membrane
Similarity search - Function
HYR domain / HYR domain profile. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. ...HYR domain / HYR domain profile. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / STAUROSPORINE / TK/RTKC protein kinase
Similarity search - Component
Biological speciesMonosiga brevicollis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBajaj, T. / Gee, C.L. / Kuriyan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Plos One / Year: 2023
Title: Crystal structure of the kinase domain of a receptor tyrosine kinase from a choanoflagellate, Monosiga brevicollis.
Authors: Bajaj, T. / Kuriyan, J. / Gee, C.L.
History
DepositionAug 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RTKC8 Kinase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8734
Polymers31,8451
Non-polymers1,0283
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.059, 55.513, 60.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein RTKC8 Kinase domain


Mass: 31845.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monosiga brevicollis (eukaryote) / Gene: 34458 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A9VBW0
#2: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.92 %
Description: Flat triangular shaped, size 10x70x100x microns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M SPG (Succinic acid, sodium dihydrogen phosphate and glycine) buffer pH 6.0, 25% (w/v) PEG 1500 Mixed 1:1 Protein: 10-15mg/mL in 50mM Tris pH 8.0, 200mM NaCl, 10% Glycerol, 0.5mM TCEP.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.95→48.555 Å / Num. obs: 20593 / % possible obs: 99.9 % / Redundancy: 26.2 % / Biso Wilson estimate: 32.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.046 / Rrim(I) all: 0.235 / Χ2: 0.95 / Net I/σ(I): 12.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 17 % / Rmerge(I) obs: 3.648 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1414 / CC1/2: 0.455 / Rpim(I) all: 0.883 / Rrim(I) all: 3.758 / Χ2: 0.76 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSVersion Jan 26, 2018data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UEU

4ueu


Resolution: 1.95→48.55 Å / SU ML: 0.2722 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 1039 5.06 %
Rwork0.2039 19497 -
obs0.2064 20536 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 75 100 2280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712246
X-RAY DIFFRACTIONf_angle_d0.84693071
X-RAY DIFFRACTIONf_chiral_restr0.054334
X-RAY DIFFRACTIONf_plane_restr0.0078380
X-RAY DIFFRACTIONf_dihedral_angle_d15.7246815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.050.31961420.29012734X-RAY DIFFRACTION99.62
2.05-2.180.32961610.28152712X-RAY DIFFRACTION99.69
2.18-2.350.25571490.2132760X-RAY DIFFRACTION99.97
2.35-2.590.28351470.22632732X-RAY DIFFRACTION99.76
2.59-2.960.29181520.2212783X-RAY DIFFRACTION99.97
2.96-3.730.25091400.20192828X-RAY DIFFRACTION99.9
3.73-48.550.21711480.17112948X-RAY DIFFRACTION99.87

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