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- PDB-8xpg: The Crystal Structure of polo box domain of Plk4 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xpg
TitleThe Crystal Structure of polo box domain of Plk4 from Biortus.
ComponentsSerine/threonine-protein kinase PLK4
KeywordsCELL CYCLE / Serine/threonine-protein kinase / Transferase
Function / homology
Function and homology information


de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / XY body / centriole replication / cleavage furrow ...de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / XY body / centriole replication / cleavage furrow / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / mitotic spindle organization / kinetochore / spindle pole / Regulation of PLK1 Activity at G2/M Transition / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / ATP binding / identical protein binding / cytosol
Similarity search - Function
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 ...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. / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of polo box domain of Plk4 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Zhang, B.
History
DepositionJan 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK4
B: Serine/threonine-protein kinase PLK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,54710
Polymers52,7782
Non-polymers7698
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-115 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.304, 77.614, 120.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-1044-

HOH

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Components

#1: Protein Serine/threonine-protein kinase PLK4 / Polo-like kinase 4 / PLK-4 / Serine/threonine-protein kinase 18 / Serine/threonine-protein kinase Sak


Mass: 26389.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18 / Production host: Escherichia coli (E. coli) / References: UniProt: O00444, polo kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.00M Ammonium sulfate, 100mM TRIS, pH7.0, 200mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.59 Å / Num. obs: 16692 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 15.1
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.031 / Num. unique obs: 2170

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 12.593 / SU ML: 0.258 / Cross valid method: FREE R-VALUE / ESU R: 1.436 / ESU R Free: 0.351
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2603 861 5.167 %
Rwork0.2086 15802 -
all0.211 --
obs-16663 99.922 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.247 Å2
Baniso -1Baniso -2Baniso -3
1--1.477 Å2-0 Å20 Å2
2--1.442 Å2-0 Å2
3---0.034 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 40 120 3799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163449
X-RAY DIFFRACTIONr_angle_refined_deg0.8741.665075
X-RAY DIFFRACTIONr_angle_other_deg0.2961.5638077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8455444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.479529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04710690
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.22810170
X-RAY DIFFRACTIONr_chiral_restr0.0380.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined0.1910.2600
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23060
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21782
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.216
X-RAY DIFFRACTIONr_nbd_other0.1280.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.27
X-RAY DIFFRACTIONr_mcbond_it3.1936.4481782
X-RAY DIFFRACTIONr_mcbond_other3.1936.4481782
X-RAY DIFFRACTIONr_mcangle_it5.2779.6642224
X-RAY DIFFRACTIONr_mcangle_other5.2769.6652225
X-RAY DIFFRACTIONr_scbond_it3.1716.9491973
X-RAY DIFFRACTIONr_scbond_other3.1366.8861942
X-RAY DIFFRACTIONr_scangle_it5.31310.242851
X-RAY DIFFRACTIONr_scangle_other5.29210.142804
X-RAY DIFFRACTIONr_lrange_it8.97578.0113952
X-RAY DIFFRACTIONr_lrange_other8.96577.3183942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.292490.2631169X-RAY DIFFRACTION99.7543
2.77-2.8460.389740.2871087X-RAY DIFFRACTION99.9139
2.846-2.9280.277580.2721079X-RAY DIFFRACTION99.8244
2.928-3.0180.347670.2621047X-RAY DIFFRACTION99.9103
3.018-3.1160.343420.2351049X-RAY DIFFRACTION99.9084
3.116-3.2250.305500.221986X-RAY DIFFRACTION100
3.225-3.3460.249540.216952X-RAY DIFFRACTION100
3.346-3.4820.275580.204928X-RAY DIFFRACTION100
3.482-3.6360.238560.201873X-RAY DIFFRACTION100
3.636-3.8130.224420.193857X-RAY DIFFRACTION100
3.813-4.0170.29370.202825X-RAY DIFFRACTION100
4.017-4.2590.237520.189749X-RAY DIFFRACTION100
4.259-4.5510.188370.175739X-RAY DIFFRACTION99.8713
4.551-4.9120.249430.171686X-RAY DIFFRACTION100
4.912-5.3750.37240.208631X-RAY DIFFRACTION100
5.375-6.0010.327360.255586X-RAY DIFFRACTION100
6.001-6.9110.307210.24526X-RAY DIFFRACTION100
6.911-8.4220.17230.177444X-RAY DIFFRACTION100
8.422-11.7360.157240.144356X-RAY DIFFRACTION100
11.736-480.31140.31233X-RAY DIFFRACTION100

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