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- PDB-1mg4: STRUCTURE OF N-TERMINAL DOUBLECORTIN DOMAIN FROM DCLK: WILD TYPE ... -

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Basic information

Entry
Database: PDB / ID: 1mg4
TitleSTRUCTURE OF N-TERMINAL DOUBLECORTIN DOMAIN FROM DCLK: WILD TYPE PROTEIN
ComponentsDOUBLECORTIN-LIKE KINASE (N-TERMINAL DOMAIN)
KeywordsTRANSFERASE / DCX Domain / Doublecortin-like Kinase / Microtubule Bundling / Cortex Development
Function / homology
Function and homology information


central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / endosomal transport / dendrite morphogenesis / regulation of postsynapse assembly / protein localization to nucleus / forebrain development / central nervous system development / response to virus ...central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / endosomal transport / dendrite morphogenesis / regulation of postsynapse assembly / protein localization to nucleus / forebrain development / central nervous system development / response to virus / neuron migration / nervous system development / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Doublecortin domain / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Doublecortin domain / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.504 Å
AuthorsKim, M.H. / Cierpickil, T. / Derewenda, U. / Krowarsch, D. / Feng, Y. / Devedjiev, Y. / Dauter, Z. / Walsh, C.A. / Otlewski, J. / Bushweller, J.H. / Derewenda, Z.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: The DCX-domain Tandems of Doublecortin and Doublecortin-like Kinase
Authors: Kim, M.H. / Cierpickil, T. / Derewenda, U. / Krowarsch, D. / Feng, Y. / Devedjiev, Y. / Dauter, Z. / Walsh, C.A. / Otlewski, J. / Bushweller, J.H. / Derewenda, Z.
History
DepositionAug 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / 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

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Assembly

Deposited unit
A: DOUBLECORTIN-LIKE KINASE (N-TERMINAL DOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0703
Polymers12,8781
Non-polymers1922
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.981, 29.621, 40.332
Angle α, β, γ (deg.)90.00, 101.33, 90.00
Int Tables number5
Space group name H-MC121
DetailsBIOLOGICAL ASSEMBLY IS A TANDEM OF N-TERMINAL AND C-TERMINAL DOMAINS

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Components

#1: Protein DOUBLECORTIN-LIKE KINASE (N-TERMINAL DOMAIN) / Doublecortin


Mass: 12877.623 Da / Num. of mol.: 1 / Fragment: (N-Terminal Domain), Residues 49-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O15075
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.95 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: CITRATE BUFFER, AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.8-2.0 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9187 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2002 / Details: Double crystal focusing mirrors
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9187 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 15460 / Num. obs: 15460 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1368 / % possible all: 85.7
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. measured all: 47701
Reflection shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.55 Å / % possible obs: 85.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MFW

1mfw


Resolution: 1.504→19.28 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.745 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.095 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18694 770 5 %RANDOM
Rwork0.15297 ---
obs0.15472 15460 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.754 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20.57 Å2
2---0.91 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.504→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms829 0 10 140 979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022847
X-RAY DIFFRACTIONr_bond_other_d0.0010.02761
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9721144
X-RAY DIFFRACTIONr_angle_other_deg2.09531776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9453100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.98415162
X-RAY DIFFRACTIONr_chiral_restr0.1190.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02920
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02178
X-RAY DIFFRACTIONr_nbd_refined0.260.3144
X-RAY DIFFRACTIONr_nbd_other0.2230.3712
X-RAY DIFFRACTIONr_nbtor_other0.170.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.528
X-RAY DIFFRACTIONr_mcbond_it1.361.5502
X-RAY DIFFRACTIONr_mcangle_it2.2242819
X-RAY DIFFRACTIONr_scbond_it2.6023345
X-RAY DIFFRACTIONr_scangle_it4.064.5325
X-RAY DIFFRACTIONr_rigid_bond_restr1.5772847
X-RAY DIFFRACTIONr_sphericity_free2.9332140
X-RAY DIFFRACTIONr_sphericity_bonded1.9482833
LS refinement shellResolution: 1.504→1.543 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.218 37
Rwork0.19 849
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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