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- PDB-4nk7: Crystal Structure of the D. melanogaster Plk4 cryptic polo box (CPB) -

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Basic information

Entry
Database: PDB / ID: 4nk7
TitleCrystal Structure of the D. melanogaster Plk4 cryptic polo box (CPB)
ComponentsSerine/threonine-protein kinase PLK4
KeywordsTRANSFERASE / cryptic polo box / Plk4 targeting / rocentrioles / asterless N-terminus / centrosomes
Function / homology
Function and homology information


syncytial blastoderm mitotic cell cycle / sperm axoneme assembly / regulation of centriole replication / polo kinase / male meiotic nuclear division / centrosome cycle / centriole replication / centriole / mitotic spindle organization / regulation of protein stability ...syncytial blastoderm mitotic cell cycle / sperm axoneme assembly / regulation of centriole replication / polo kinase / male meiotic nuclear division / centrosome cycle / centriole replication / centriole / mitotic spindle organization / regulation of protein stability / kinetochore / spindle pole / positive regulation of protein catabolic process / protein autophosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Arylsulfatase, C-terminal domain - #120 / Arylsulfatase, C-terminal domain - #130 / Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 ...Arylsulfatase, C-terminal domain - #120 / Arylsulfatase, C-terminal domain - #130 / Serine/threonine-protein kinase, first cryptic polo-box domain superfamily / : / Cryptic Polo-Box 1 (CPB1) domain profile. / Cryptic Polo-Box 2 (CPB2) domain profile. / Plk4, C-terminal polo-box domain / Plk4, second cryptic polo-box domain / Plk4, first cryptic polo-box domain / Polo-like Kinase 4 Polo Box 1 / Polo-like Kinase 4 Polo Box 2 / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / Tyrosine-protein kinase, active site / Protein kinase 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 / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK4
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.233 Å
AuthorsDong, G. / Lesigang, J.
CitationJournal: Structure / Year: 2014
Title: Structure of the C. elegans ZYG-1 Cryptic Polo Box Suggests a Conserved Mechanism for Centriolar Docking of Plk4 Kinases.
Authors: Shimanovskaya, E. / Viscardi, V. / Lesigang, J. / Lettman, M.M. / Qiao, R. / Svergun, D.I. / Round, A. / Oegema, K. / Dong, G.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)25,4981
Polymers25,4981
Non-polymers00
Water0
1
A: Serine/threonine-protein kinase PLK4

A: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)50,9972
Polymers50,9972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_557x-y,-y,-z+21
Buried area1570 Å2
ΔGint-8 kcal/mol
Surface area25260 Å2
MethodPISA
2
A: Serine/threonine-protein kinase PLK4

A: Serine/threonine-protein kinase PLK4

A: Serine/threonine-protein kinase PLK4

A: Serine/threonine-protein kinase PLK4


Theoretical massNumber of molelcules
Total (without water)101,9934
Polymers101,9934
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_557x-y,-y,-z+21
crystal symmetry operation11_657-x+y+1,y,-z+21
Buried area4710 Å2
ΔGint-28 kcal/mol
Surface area48950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.207, 132.207, 134.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase SAK


Mass: 25498.285 Da / Num. of mol.: 1 / Fragment: cryptic polo box, UNP residues 383-601
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG7186, D. melanogaster Plk4 (residues 383-601), SAK / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O97143, polo kinase

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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: 6.64 Å3/Da / Density % sol: 81.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES-NaOH (pH 7.0), 2.5 M NaCl, 2 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2012 / Details: Toroidal focusing mirror
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. all: 11619 / Num. obs: 11543 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 41.8 %
Reflection shellResolution: 3.23→3.43 Å / Redundancy: 41.6 % / Mean I/σ(I) obs: 0.97 / Num. unique all: 73134 / % possible all: 96.4

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Processing

Software
NameVersionClassification
DNAdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G7N

4g7n


Resolution: 3.233→19.875 Å / SU ML: 0.8 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 34.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 2076 9.98 %RANDOM
Rwork0.2403 ---
obs0.2426 11527 99.5 %-
all-20915 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.233→19.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 0 0 1705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061742
X-RAY DIFFRACTIONf_angle_d1.0592353
X-RAY DIFFRACTIONf_dihedral_angle_d14.83677
X-RAY DIFFRACTIONf_chiral_restr0.061258
X-RAY DIFFRACTIONf_plane_restr0.007304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.233-3.30790.55771260.50221165X-RAY DIFFRACTION94
3.3079-3.39020.38951450.42581265X-RAY DIFFRACTION100
3.3902-3.48140.37831390.36411245X-RAY DIFFRACTION100
3.4814-3.58330.33251360.33051254X-RAY DIFFRACTION100
3.5833-3.69820.32881420.31061253X-RAY DIFFRACTION100
3.6982-3.82950.30431380.27971255X-RAY DIFFRACTION100
3.8295-3.98160.25621410.25961248X-RAY DIFFRACTION100
3.9816-4.16130.27551290.23761268X-RAY DIFFRACTION100
4.1613-4.37840.2881390.20561245X-RAY DIFFRACTION100
4.3784-4.64950.18631440.18551246X-RAY DIFFRACTION100
4.6495-5.00320.221360.20191264X-RAY DIFFRACTION100
5.0032-5.4970.24471390.21751253X-RAY DIFFRACTION100
5.497-6.27040.29241400.21781267X-RAY DIFFRACTION100
6.2704-7.81920.29581400.24351257X-RAY DIFFRACTION100
7.8192-19.87550.21371420.21241249X-RAY DIFFRACTION100

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