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- PDB-6kyr: Crystal structure of DCLK1 mutant (P675L) Autoinhibited Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 6kyr
TitleCrystal structure of DCLK1 mutant (P675L) Autoinhibited Kinase Domain
ComponentsSerine/threonine-protein kinase DCLK1
KeywordsSIGNALING PROTEIN / kinase / autoinhibition
Function / homology
Function and homology information


axon extension / endosomal transport / protein localization to nucleus / central nervous system development / response to virus / nervous system development / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction ...axon extension / endosomal transport / protein localization to nucleus / central nervous system development / response to virus / nervous system development / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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
BETA-MERCAPTOETHANOL / Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 Å
AuthorsYu, Y. / Chen, Q.
CitationJournal: Innovation (N Y) / Year: 2021
Title: DCLK1 Autoinhibition and Activation in Tumorigenesis
Authors: Cheng, L. / Yang, Z. / Guo, W. / Wu, C. / Liang, S. / Tong, A. / Cao, Z. / Thorne, R.F. / Yang, S.Y. / Yu, Y. / Chen, Q.
History
DepositionSep 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase DCLK1
B: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5045
Polymers73,2702
Non-polymers2343
Water6,882382
1
A: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7913
Polymers36,6351
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-2 kcal/mol
Surface area14740 Å2
MethodPISA
2
B: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7132
Polymers36,6351
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-3 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.941, 78.003, 177.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase DCLK1 / Doublecortin domain-containing protein 3A / Doublecortin-like and CAM kinase-like 1 / Doublecortin- ...Doublecortin domain-containing protein 3A / Doublecortin-like and CAM kinase-like 1 / Doublecortin-like kinase 1


Mass: 36634.871 Da / Num. of mol.: 2 / Mutation: P675L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLK1, DCAMKL1, DCDC3A, KIAA0369 / Production host: Escherichia coli (E. coli)
References: UniProt: O15075, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.86 Å3/Da / Density % sol: 68.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6M NaH2PO4/K2HPO4, PH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.22
ReflectionResolution: 2.2→50 Å / Num. obs: 55177 / % possible obs: 100 % / Redundancy: 6.3 % / Rsym value: 0.095 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.25 Å / Num. unique obs: 3594 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FG9

4fg9


Resolution: 2.206→47.145 Å / FOM work R set: 0.8082 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.201 1229 2.26 %
Rwork0.1795 52973 -
obs0.1819 54274 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.74 Å2 / Biso mean: 35.12 Å2 / Biso min: 8.4 Å2
Refinement stepCycle: final / Resolution: 2.206→47.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4909 0 28 382 5319
Biso mean--54.75 37.91 -
Num. residues----621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035045
X-RAY DIFFRACTIONf_angle_d0.6686832
X-RAY DIFFRACTIONf_chiral_restr0.028783
X-RAY DIFFRACTIONf_plane_restr0.002871
X-RAY DIFFRACTIONf_dihedral_angle_d11.9371877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2088-2.29720.2643910.24835133522485
2.2972-2.40170.28731360.24495824596097
2.4017-2.52830.29531330.23865909604298
2.5283-2.68660.24051450.22715921606697
2.6866-2.89390.2411550.21535951610697
2.8939-3.18480.20831400.19815899603998
3.1848-3.6450.18761360.17076002613898
3.645-4.58970.15571350.13096085622098
4.5897-30.0540.1751460.15696249639597

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