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- PDB-5jzj: Crystal structure of DCLK1-KD in complex with AMPPN -

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Basic information

Entry
Database: PDB / ID: 5jzj
TitleCrystal structure of DCLK1-KD in complex with AMPPN
ComponentsSerine/threonine-protein kinase DCLK1
KeywordsTRANSFERASE / kinase / doublecortin
Function / homology
Function and homology information


central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration ...central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration / response to virus / nervous system development / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AMP PHOSPHORAMIDATE / Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsPatel, O. / Lucet, I.
CitationJournal: Structure / Year: 2016
Title: Biochemical and Structural Insights into Doublecortin-like Kinase Domain 1.
Authors: Patel, O. / Dai, W. / Mentzel, M. / Griffin, M.D. / Serindoux, J. / Gay, Y. / Fischer, S. / Sterle, S. / Kropp, A. / Burns, C.J. / Ernst, M. / Buchert, M. / Lucet, I.S.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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)67,9477
Polymers66,9502
Non-polymers9975
Water8,881493
1
A: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0224
Polymers33,4751
Non-polymers5473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase DCLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9263
Polymers33,4751
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.390, 81.270, 59.610
Angle α, β, γ (deg.)90.000, 92.100, 90.000
Int Tables number4
Space group name H-MP1211

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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: 33475.086 Da / Num. of mol.: 2 / Fragment: UNP residues 372-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLK1, DCAMKL1, DCDC3A, KIAA0369 / Plasmid: pCOLD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O15075, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5 / Details: PEG MME 5000, ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.71→56.35 Å / Num. obs: 57833 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 21.39 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.058 / Rrim(I) all: 0.132 / Net I/σ(I): 9.4 / Num. measured all: 297540 / Scaling rejects: 65
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.71-1.744.90.6961479530130.7770.3510.783399.8
9.06-56.3550.08920704140.9830.0430.09917.699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.2.7data scaling
BUSTER-TNT2.10.0refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y7J

2y7j


Resolution: 1.71→56.35 Å / Cor.coef. Fo:Fc: 0.9445 / Cor.coef. Fo:Fc free: 0.9334 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.103 / SU Rfree Cruickshank DPI: 0.101
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 2932 5.07 %RANDOM
Rwork0.1768 ---
obs0.1784 57807 99.57 %-
Displacement parametersBiso max: 95.67 Å2 / Biso mean: 25.92 Å2 / Biso min: 8.34 Å2
Baniso -1Baniso -2Baniso -3
1--3.2428 Å20 Å26.635 Å2
2--4.9689 Å20 Å2
3----1.7261 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: final / Resolution: 1.71→56.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 56 493 4648
Biso mean--18.11 35.27 -
Num. residues----533
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1950SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes621HARMONIC5
X-RAY DIFFRACTIONt_it4281HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion582SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5406SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4281HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5852HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion2.61
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2253 217 5.36 %
Rwork0.21 3831 -
all0.2109 4048 -
obs--99.57 %

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