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- PDB-4g7n: The Structure of the Plk4 Cryptic Polo Box Reveals Two Tandem Pol... -

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Basic information

Entry
Database: PDB / ID: 4g7n
TitleThe Structure of the Plk4 Cryptic Polo Box Reveals Two Tandem Polo Boxes Required for Centriole Duplication
ComponentsSerine/threonine-protein kinase PLK4
KeywordsTRANSFERASE / Polo Box / Kinase targeting and regulation / Asterless / Centriole
Function / homology
Function and homology information


syncytial blastoderm mitotic cell cycle / regulation of centriole replication / sperm axoneme assembly / polo kinase / male meiotic nuclear division / centrosome cycle / centriole replication / centriole / mitotic spindle organization / regulation of protein stability ...syncytial blastoderm mitotic cell cycle / regulation of centriole replication / sperm axoneme assembly / 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 / SAD / Resolution: 2.3 Å
AuthorsSlep, K.C. / Slevin, L.K.
CitationJournal: Structure / Year: 2012
Title: The structure of the plk4 cryptic polo box reveals two tandem polo boxes required for centriole duplication.
Authors: Slevin, L.K. / Nye, J. / Pinkerton, D.C. / Buster, D.W. / Rogers, G.C. / Slep, K.C.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references

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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)51,9978
Polymers51,4212
Non-polymers5766
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-83 kcal/mol
Surface area23610 Å2
MethodPISA
2
A: Serine/threonine-protein kinase PLK4
hetero molecules

A: Serine/threonine-protein kinase PLK4
hetero molecules

B: Serine/threonine-protein kinase PLK4
hetero molecules

B: Serine/threonine-protein kinase PLK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,99516
Polymers102,8424
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_547-x+1/2,y-1/2,-z+21
crystal symmetry operation4_557x+1/2,-y+1/2,-z+21
Buried area8360 Å2
ΔGint-174 kcal/mol
Surface area46060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.773, 135.580, 46.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 25710.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG7186, Plk4, SAK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: O97143, polo kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: an equal volume of 7.2 mg/ml Plk4 PB1-PB2 and well solution containing 1.2 M Li2SO4, 100 mM Hepes, pH 7.5 were mixed together and equilibrated over 1 ml of well solution., VAPOR DIFFUSION, ...Details: an equal volume of 7.2 mg/ml Plk4 PB1-PB2 and well solution containing 1.2 M Li2SO4, 100 mM Hepes, pH 7.5 were mixed together and equilibrated over 1 ml of well solution., VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0089 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2010
RadiationMonochromator: APS ID22 Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 2.3→31.8 Å / Num. all: 25256 / Num. obs: 22051 / % possible obs: 89.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.055 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 3.8 / Num. unique all: 1780 / Rsym value: 0.334 / % possible all: 84.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→31.776 Å / SU ML: 0.31 / σ(F): 0.1 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 1889 8.57 %10
Rwork0.1847 ---
all0.1908 25256 --
obs0.1908 22051 87.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.769 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3668 Å2-0 Å20 Å2
2---2.1324 Å2-0 Å2
3---2.4991 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 30 184 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083580
X-RAY DIFFRACTIONf_angle_d1.094839
X-RAY DIFFRACTIONf_dihedral_angle_d14.6231379
X-RAY DIFFRACTIONf_chiral_restr0.072526
X-RAY DIFFRACTIONf_plane_restr0.005622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2995-2.38170.30711500.19811630X-RAY DIFFRACTION72
2.3817-2.4770.29381730.2041819X-RAY DIFFRACTION80
2.477-2.58970.30271740.20951848X-RAY DIFFRACTION82
2.5897-2.72610.30051800.21111897X-RAY DIFFRACTION83
2.7261-2.89680.31870.21282017X-RAY DIFFRACTION88
2.8968-3.12030.29541970.2112106X-RAY DIFFRACTION92
3.1203-3.4340.27492010.19442184X-RAY DIFFRACTION95
3.434-3.93010.22022060.16612144X-RAY DIFFRACTION93
3.9301-4.94850.19252070.13532224X-RAY DIFFRACTION95
4.9485-31.77940.23852140.17662293X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 22.5707 Å / Origin y: 48.7909 Å / Origin z: 37.6371 Å
111213212223313233
T0.0791 Å20.0009 Å2-0.0144 Å2-0.0616 Å20.0414 Å2--0.1359 Å2
L0.6689 °20.3102 °20.0037 °2-0.4455 °2-0.1111 °2--0.8118 °2
S0.0835 Å °-0.0282 Å °0.0487 Å °0.1162 Å °-0.0775 Å °0.0539 Å °-0.1099 Å °0.0624 Å °-0.0059 Å °
Refinement TLS groupSelection details: all

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