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- PDB-4rs6: Crystal structure of the C domain of Polo like Kinase II in Homo ... -

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Basic information

Entry
Database: PDB / ID: 4rs6
TitleCrystal structure of the C domain of Polo like Kinase II in Homo Sapiens
ComponentsSerine/threonine-protein kinase PLK2
KeywordsTRANSFERASE / First PBD domain of Polo like Kinase II / phosphorylation of target protein
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 / CD163 mediating an anti-inflammatory response / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / 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 / CD163 mediating an anti-inflammatory response / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cellular senescence / positive regulation of autophagy / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of inflammatory response to antigenic stimulus / 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 / memory / kinetochore / 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
Serine/threonine-protein kinase PLK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShan, H. / Quan, J. / Wang, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of the polo-box domain of polo-like kinase 2
Authors: Shan, H.M. / Wang, T. / Quan, J.M.
History
DepositionNov 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,8882
Polymers54,8882
Non-polymers00
Water25214
1
A: Serine/threonine-protein kinase PLK2


Theoretical massNumber of molelcules
Total (without water)27,4441
Polymers27,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PLK2


Theoretical massNumber of molelcules
Total (without water)27,4441
Polymers27,4441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.075, 153.075, 153.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.797687, 0.386748, -0.462732), (0.302483, -0.407216, -0.861788), (-0.521727, -0.827406, 0.207846)-38.24932, -59.96606, -57.5525

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Components

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


Mass: 27444.088 Da / Num. of mol.: 2 / Fragment: PBD domain, UNP residues 451-685
Source method: isolated from a genetically manipulated source
Details: inserted between EcoRI and XhoI, protease cleavage to remove GST tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK2, SNK / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NYY3, polo kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 18474 / Num. obs: 17518 / % possible obs: 88 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21.8 % / Rmerge(I) obs: 0.16 / Rsym value: 0.15
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.6-2.640.861.50.841100
7.01-250.15270.121100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J7B

4j7b


Resolution: 2.6→24.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 22.591 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.478 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24724 947 5.1 %RANDOM
Rwork0.18595 ---
obs0.18891 17518 99.83 %-
all-18474 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.497 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 14 3462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193528
X-RAY DIFFRACTIONr_bond_other_d0.0010.023280
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9534782
X-RAY DIFFRACTIONr_angle_other_deg0.88837550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7885424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10524.471170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8715614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1731516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02838
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 82 -
Rwork0.317 1236 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.56730.44761.9782.84310.14656.6787-0.07850.0737-0.43520.21010.2908-0.0432-0.0940.1769-0.21230.0827-0.03470.06310.0869-0.02190.2303-19.1653-55.0548-10.6011
25.66222.8236-3.30816.6431-3.22244.156-0.08960.18740.47220.12340.37880.236-0.2637-0.4921-0.28920.2370.0769-0.0230.18120.10040.1146-38.2322-33.4712-3.3083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A470 - 682
2X-RAY DIFFRACTION2B470 - 682

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