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- PDB-1mby: Murine Sak Polo Domain -

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Basic information

Entry
Database: PDB / ID: 1mby
TitleMurine Sak Polo Domain
Componentsserine/threonine kinaseSerine/threonine-specific protein kinase
KeywordsTRANSFERASE / POLO DOMAIN / STRAND EXCHANGE
Function / homology
Function and homology information


de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / deuterosome / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane ...de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / deuterosome / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / XY body / centriole replication / cleavage furrow / centriole / regulation of cytokinesis / spindle pole / mitotic cell cycle / protein phosphorylation / protein serine/threonine kinase activity / centrosome / nucleolus / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase Plk4 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #930 / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Serine/threonine-protein kinase Plk4 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #930 / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLeung, G.C. / Hudson, J.W. / Kozarova, A. / Davidson, A. / Dennis, J.W. / Sicheri, F.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The Sak polo-box comprises a structural domain sufficient for mitotic subcellular localization.
Authors: Leung, G.C. / Hudson, J.W. / Kozarova, A. / Davidson, A. / Dennis, J.W. / Sicheri, F.
History
DepositionAug 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: serine/threonine kinase
B: serine/threonine kinase


Theoretical massNumber of molelcules
Total (without water)19,3242
Polymers19,3242
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-22 kcal/mol
Surface area9300 Å2
MethodPISA
2
A: serine/threonine kinase
B: serine/threonine kinase

A: serine/threonine kinase
B: serine/threonine kinase


Theoretical massNumber of molelcules
Total (without water)38,6484
Polymers38,6484
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+1/31
Buried area7020 Å2
ΔGint-57 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.782, 51.782, 146.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein serine/threonine kinase / Serine/threonine-specific protein kinase / SAK


Mass: 9661.930 Da / Num. of mol.: 2 / Fragment: Polo domain (residues 839-925) / Mutation: C909L, V874M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sak / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 BL21 / References: UniProt: Q64702, EC: 2.7.1.37
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Jeffamine M-600, magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mg/mlprotein1drop
220 mMHEPES1droppH8.0
35 mMdithiothreitol1drop
4100 mMTris1reservoirpH7.0
532.5 %(v/v)Jeffamine M-6001reservoir
6200 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9788,0.9790,0.9637,0.9945
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 13, 2000
RadiationMonochromator: crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.9791
30.96371
40.99451

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2839 -random
Rwork0.231 ---
all-29811 --
obs-29274 98.2 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 0 58 1224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.539
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. reflection all: 15511 / Num. reflection obs: 14153 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.2265 / Rfactor Rfree: 0.2475 / Rfactor Rwork: 0.2185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.51

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