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- PDB-6vg3: Structure of unliganded, inactive PTK7 kinase domain -

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Basic information

Entry
Database: PDB / ID: 6vg3
TitleStructure of unliganded, inactive PTK7 kinase domain
ComponentsInactive tyrosine-protein kinase 7
KeywordsTRANSFERASE / Kinase / Pseudokinase / Autoinhibition
Function / homology
Function and homology information


axis elongation / : / convergent extension / : / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / establishment of planar polarity / coronary vasculature development / lung-associated mesenchyme development / establishment of epithelial cell apical/basal polarity ...axis elongation / : / convergent extension / : / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / establishment of planar polarity / coronary vasculature development / lung-associated mesenchyme development / establishment of epithelial cell apical/basal polarity / ventricular septum development / plasma membrane => GO:0005886 / cellular response to retinoic acid / kidney development / wound healing / positive regulation of neuron projection development / cell-cell junction / positive regulation of canonical Wnt signaling pathway / cell migration / cell adhesion / protein kinase activity / focal adhesion / signal transduction / ATP binding
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain ...Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 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
Inactive tyrosine-protein kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsMalhotra, K. / Stayrook, S.E. / Sheetz, J. / Lemmon, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122485 United States
CitationJournal: Mol.Cell / Year: 2020
Title: Structural insights into receptor tyrosine kinase pseudokinase function
Authors: Sheetz, J.B. / Mathea, S. / Karvonen, H. / Malhotra, K. / Chaterjee, D. / Perttila, R. / Niininen, W. / Stayrook, S.E. / Radhakrishnan, R. / Ungureanu, D. / Knapp, S. / Lemmon, M.A.
History
DepositionJan 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inactive tyrosine-protein kinase 7
B: Inactive tyrosine-protein kinase 7
C: Inactive tyrosine-protein kinase 7


Theoretical massNumber of molelcules
Total (without water)99,8523
Polymers99,8523
Non-polymers00
Water11,620645
1
A: Inactive tyrosine-protein kinase 7


Theoretical massNumber of molelcules
Total (without water)33,2841
Polymers33,2841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inactive tyrosine-protein kinase 7


Theoretical massNumber of molelcules
Total (without water)33,2841
Polymers33,2841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Inactive tyrosine-protein kinase 7


Theoretical massNumber of molelcules
Total (without water)33,2841
Polymers33,2841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.628, 119.918, 166.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Inactive tyrosine-protein kinase 7 / Colon carcinoma kinase 4 / CCK-4 / Protein-tyrosine kinase 7 / Pseudo tyrosine kinase receptor 7 / ...Colon carcinoma kinase 4 / CCK-4 / Protein-tyrosine kinase 7 / Pseudo tyrosine kinase receptor 7 / Tyrosine-protein kinase-like 7


Mass: 33283.996 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK7, CCK4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13308
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11 mg/ml protein, 100 mM ADA (pH 6.5), 100 mM (NH4)2SO4, 30% (w/v) PEG monoethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2017 / Details: undulator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→135.355 Å / Num. obs: 68916 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 36.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.101 / Rrim(I) all: 0.199 / Rsym value: 0.171 / Net I/av σ(I): 3.9 / Net I/σ(I): 5.2
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.024 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 9835 / CC1/2: 0.738 / Rpim(I) all: 0.443 / Rsym value: 1.209 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.98 Å48.63 Å
Translation3.98 Å48.63 Å

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Processing

Software
NameVersionClassification
XDSMar 15, 2019 BUILT=20190315data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LUF

1luf


Resolution: 1.95→48.66 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3335 4.84 %RANDOM
Rwork0.189 ---
obs0.192 68916 98.5 %-
Displacement parametersBiso max: 145.16 Å2 / Biso mean: 43.69 Å2 / Biso min: 20.83 Å2
Baniso -1Baniso -2Baniso -3
1-9.6787 Å20 Å20 Å2
2---14.7223 Å20 Å2
3---5.0436 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.95→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 0 645 7161
Biso mean---50.79 -
Num. residues----821
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2380SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1126HARMONIC5
X-RAY DIFFRACTIONt_it6655HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion803SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_ideal_dist_contact7872SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6655HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8975HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion17.65
LS refinement shellResolution: 1.95→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2693 58 4.21 %
Rwork0.2605 1321 -
all0.2608 1379 -
obs--91.52 %

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