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- PDB-8xb9: The Crystal Structure of polo-box domain of PLK1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xb9
TitleThe Crystal Structure of polo-box domain of PLK1 from Biortus.
ComponentsSerine/threonine-protein kinase PLK1
KeywordsTRANSFERASE / Serine/threonine-protein kinase
Function / homology
Function and homology information


Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / nuclear membrane disassembly / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / nuclear membrane disassembly / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / regulation of protein binding / anaphase-promoting complex binding / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / mitotic chromosome condensation / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic cytokinesis / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / RHO GTPases Activate Formins / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / kinetochore / spindle pole / spindle / positive regulation of protein localization to nucleus / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / peptidyl-serine phosphorylation / protein ubiquitination / regulation of cell cycle / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / 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
Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, F. / Cheng, W. / Yuan, 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 PLK1 from Biortus
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Meng, Q. / Zhang, B.
History
DepositionDec 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3472
Polymers27,2851
Non-polymers621
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.181, 92.786, 35.890
Angle α, β, γ (deg.)90.000, 101.642, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 27285.158 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 371-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli (E. coli) / References: UniProt: P53350, polo kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 31% PEG3350, 0.1M Bis Tris pH 5.8

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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 PILATUS3 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: 1.95→46.39 Å / Num. obs: 15223 / % possible obs: 98.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.7
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.328 / Num. unique obs: 1066

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.176 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.606 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.199 / ESU R Free: 0.178
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2448 756 4.974 %
Rwork0.1885 14443 -
all0.191 --
obs-15199 97.894 %
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: 44.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.258 Å2-0 Å21.802 Å2
2---0.381 Å2-0 Å2
3----0.095 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 4 90 1897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121852
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161683
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6522502
X-RAY DIFFRACTIONr_angle_other_deg0.4681.5663925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.373517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44210335
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.2791088
X-RAY DIFFRACTIONr_chiral_restr0.0620.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
X-RAY DIFFRACTIONr_nbd_refined0.220.2353
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21611
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2910
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.224
X-RAY DIFFRACTIONr_nbd_other0.1850.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3160.27
X-RAY DIFFRACTIONr_mcbond_it4.0244.419886
X-RAY DIFFRACTIONr_mcbond_other4.0164.418886
X-RAY DIFFRACTIONr_mcangle_it5.5026.5951105
X-RAY DIFFRACTIONr_mcangle_other5.56.61106
X-RAY DIFFRACTIONr_scbond_it4.5965.042966
X-RAY DIFFRACTIONr_scbond_other4.5955.044967
X-RAY DIFFRACTIONr_scangle_it6.967.3351395
X-RAY DIFFRACTIONr_scangle_other6.9587.3371396
X-RAY DIFFRACTIONr_lrange_it9.70175.5922131
X-RAY DIFFRACTIONr_lrange_other9.71575.2822113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.397560.24610450.25311360.9080.96196.9190.224
2.001-2.0550.269570.24410310.24511250.9540.96296.71110.223
2.055-2.1150.275430.2379920.23910660.9510.96597.09190.222
2.115-2.1790.36490.239740.23510470.9240.96897.70770.217
2.179-2.2510.236390.2159690.21610410.970.97296.830.204
2.251-2.3290.26440.2189150.229800.9550.96997.85710.209
2.329-2.4170.275550.28710.2059500.9460.97597.47370.2
2.417-2.5150.218490.1898430.1919080.9710.97898.23790.196
2.515-2.6260.217380.1958270.1968820.9670.97798.07260.204
2.626-2.7540.337430.1987960.2048580.9450.97697.78560.216
2.754-2.9020.221480.2067300.2077880.9650.97498.7310.231
2.902-3.0760.267300.2147080.2167510.9380.9798.2690.246
3.076-3.2870.247410.2186750.227250.9630.97298.75860.255
3.287-3.5480.252300.2026230.2056600.9710.97598.93940.234
3.548-3.8820.31310.1845680.1916060.9480.97998.84490.224
3.882-4.3340.213290.1445190.1485560.9720.98798.56110.187
4.334-4.9920.175340.1414570.1434930.9830.98899.59430.194
4.992-6.0830.218210.1713990.1744230.9610.98399.29080.235
6.083-8.4770.234130.1843170.1863350.9690.9898.50750.243
8.477-35.1760.20560.1431840.1451950.9790.98597.43590.198

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