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- PDB-4xb0: Structure of the Plk2 polo-box domain -

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Basic information

Entry
Database: PDB / ID: 4xb0
TitleStructure of the Plk2 polo-box domain
ComponentsSerine/threonine-protein kinase PLK2
KeywordsTRANSFERASE / polo-box domain / Polo-like kinase 2 / Plk2
Function / homology
Function and homology information


regulation of centriole replication / Rap protein signal transduction / negative regulation of apoptotic process in bone marrow cell / polo kinase / ATP-dependent protein binding / long-term synaptic depression / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / CD163 mediating an anti-inflammatory response / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cellular senescence ...regulation of centriole replication / Rap protein signal transduction / negative regulation of apoptotic process in bone marrow cell / polo kinase / ATP-dependent protein binding / long-term synaptic depression / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / CD163 mediating an anti-inflammatory response / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cellular senescence / positive regulation of autophagy / negative regulation of inflammatory response to antigenic stimulus / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / centriole / negative regulation of angiogenesis / mitotic spindle organization / long-term synaptic potentiation / regulation of synaptic plasticity / G1/S transition of mitotic cell cycle / kinetochore / memory / spindle pole / positive regulation of protein catabolic process / peptidyl-serine phosphorylation / positive regulation of canonical NF-kappaB signal transduction / Ras protein signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / chromatin / negative regulation of apoptotic process / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
PLK2, catalytic domain / POLO box domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / Serine/threonine-protein kinase, active site ...PLK2, catalytic domain / POLO box domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / 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 / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Serine/threonine-protein kinase PLK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsKim, J.H. / Ku, B. / Kim, S.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea2011-0030027 Korea, Republic Of
Korea Research Institute of Bioscience and Biotechnology Research Initiative Program Korea, Republic Of
CitationJournal: Proteins / Year: 2015
Title: Structural analysis of the polo-box domain of human Polo-like kinase 2
Authors: Kim, J.H. / Ku, B. / Lee, K.S. / Kim, S.J.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PLK2
B: Serine/threonine-protein kinase PLK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4895
Polymers50,3232
Non-polymers1663
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-5 kcal/mol
Surface area21310 Å2
Unit cell
Length a, b, c (Å)152.292, 152.292, 152.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Serine/threonine-protein kinase PLK2 / Polo-like kinase 2 / hPlk2 / Serine/threonine-protein kinase SNK / hSNK / Serum-inducible kinase


Mass: 25161.703 Da / Num. of mol.: 2 / Fragment: polo-box domain, UNP residues 468-685
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK2, SNK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9NYY3, polo kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.26 M sodium phosphate, 0.14 M potassium phosphate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 16508 / % possible obs: 99.6 % / Redundancy: 22.1 % / Net I/σ(I): 48.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the polo-box domain of Plk1

Resolution: 2.701→26.922 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.76 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 1622 10 %
Rwork0.2251 --
obs0.2289 16221 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→26.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 7 22 3467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043522
X-RAY DIFFRACTIONf_angle_d1.0484774
X-RAY DIFFRACTIONf_dihedral_angle_d15.9521284
X-RAY DIFFRACTIONf_chiral_restr0.039528
X-RAY DIFFRACTIONf_plane_restr0.004606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7006-2.780.3641340.33681197X-RAY DIFFRACTION99
2.78-2.86960.34921340.31071216X-RAY DIFFRACTION99
2.8696-2.97210.3261320.28621193X-RAY DIFFRACTION99
2.9721-3.09090.30361310.27331190X-RAY DIFFRACTION100
3.0909-3.23140.31811390.26711212X-RAY DIFFRACTION100
3.2314-3.40140.26911350.24991206X-RAY DIFFRACTION100
3.4014-3.61410.27671300.2381214X-RAY DIFFRACTION100
3.6141-3.89230.26211350.21861208X-RAY DIFFRACTION100
3.8923-4.28260.22811370.19171225X-RAY DIFFRACTION100
4.2826-4.89910.20071380.17211223X-RAY DIFFRACTION100
4.8991-6.16020.25171370.22221241X-RAY DIFFRACTION100
6.1602-26.9230.24941400.19661274X-RAY DIFFRACTION100

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