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- PDB-4nkb: Crystal Structure of the cryptic polo box (CPB)of ZYG-1 -

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Basic information

Entry
Database: PDB / ID: 4nkb
TitleCrystal Structure of the cryptic polo box (CPB)of ZYG-1
ComponentsProbable serine/threonine-protein kinase zyg-1
KeywordsTRANSFERASE / cryptic polo box / Centriole biogenesis / centrosomes
Function / homology
Function and homology information


activation of mitotic cell cycle spindle assembly checkpoint / regulation of mitotic cytokinetic process / Polo-like kinase mediated events / Cyclin A/B1/B2 associated events during G2/M transition / G2/M DNA replication checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of mitotic cell cycle, embryonic / positive regulation of mitotic cell cycle, embryonic / regulation of spindle assembly / : ...activation of mitotic cell cycle spindle assembly checkpoint / regulation of mitotic cytokinetic process / Polo-like kinase mediated events / Cyclin A/B1/B2 associated events during G2/M transition / G2/M DNA replication checkpoint / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of mitotic cell cycle, embryonic / positive regulation of mitotic cell cycle, embryonic / regulation of spindle assembly / : / detection of temperature stimulus / positive regulation of centrosome duplication / regulation of protein localization to centrosome / protein localization => GO:0008104 / positive regulation of protein localization to kinetochore / centriole replication / positive regulation of spindle assembly / centrosome duplication / regulation of centrosome duplication / embryo development ending in birth or egg hatching / spindle assembly / centriole / protein localization / mitotic cell cycle / peptidyl-serine phosphorylation / regulation of cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein serine/threonine kinase activity / centrosome / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Zyg-1, polo box domain 1 / Zyg-1, polo box domain 2 / Polo box domain / Polo box domain / Arylsulfatase, C-terminal domain - #120 / Arylsulfatase, C-terminal domain - #130 / Arylsulfatase, C-terminal domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain ...Zyg-1, polo box domain 1 / Zyg-1, polo box domain 2 / Polo box domain / Polo box domain / Arylsulfatase, C-terminal domain - #120 / Arylsulfatase, C-terminal domain - #130 / Arylsulfatase, C-terminal domain / Tyrosine protein kinases specific active-site signature. / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Probable serine/threonine-protein kinase zyg-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsShimanovskaya, E. / Dong, G.
CitationJournal: Structure / Year: 2014
Title: Structure of the C. elegans ZYG-1 Cryptic Polo Box Suggests a Conserved Mechanism for Centriolar Docking of Plk4 Kinases.
Authors: Shimanovskaya, E. / Viscardi, V. / Lesigang, J. / Lettman, M.M. / Qiao, R. / Svergun, D.I. / Round, A. / Oegema, K. / Dong, G.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable serine/threonine-protein kinase zyg-1
B: Probable serine/threonine-protein kinase zyg-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9828
Polymers52,4792
Non-polymers5046
Water4,071226
1
A: Probable serine/threonine-protein kinase zyg-1
hetero molecules

B: Probable serine/threonine-protein kinase zyg-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9828
Polymers52,4792
Non-polymers5046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2320 Å2
ΔGint-27 kcal/mol
Surface area22130 Å2
MethodPISA
2
A: Probable serine/threonine-protein kinase zyg-1
B: Probable serine/threonine-protein kinase zyg-1
hetero molecules

A: Probable serine/threonine-protein kinase zyg-1
B: Probable serine/threonine-protein kinase zyg-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,96416
Polymers104,9574
Non-polymers1,00712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8680 Å2
ΔGint-67 kcal/mol
Surface area40230 Å2
MethodPISA
3
A: Probable serine/threonine-protein kinase zyg-1
hetero molecules

A: Probable serine/threonine-protein kinase zyg-1
hetero molecules

B: Probable serine/threonine-protein kinase zyg-1
hetero molecules

B: Probable serine/threonine-protein kinase zyg-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,96416
Polymers104,9574
Non-polymers1,00712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area8200 Å2
ΔGint-93 kcal/mol
Surface area41100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.383, 60.093, 87.515
Angle α, β, γ (deg.)90.00, 93.31, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-776-

HOH

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Components

#1: Protein Probable serine/threonine-protein kinase zyg-1 / Zygote defective protein 1


Mass: 26239.324 Da / Num. of mol.: 2 / Fragment: UNP residues 338-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C. elegans ZYG-1 (residues 338-564), F59E12.2, zyg-1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9GT24, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 53.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM tri-sodium citrate (pH 5.6), 15% (w/v) PEG 4,000, 200 mM (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2011 / Details: channel-cut crystal
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 48287 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 %
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.53 / Num. unique all: 7837 / % possible all: 96.2

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Processing

Software
NameVersionClassification
DNAdata collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→24.957 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 31.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 3343 7.09 %RANDOM
Rwork0.2435 ---
obs0.2457 47167 97.78 %-
all-48238 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→24.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 27 226 3487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043315
X-RAY DIFFRACTIONf_angle_d0.8764454
X-RAY DIFFRACTIONf_dihedral_angle_d12.9871285
X-RAY DIFFRACTIONf_chiral_restr0.059488
X-RAY DIFFRACTIONf_plane_restr0.005583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33290.44151210.36641842X-RAY DIFFRACTION98
2.3329-2.36770.42571430.35241866X-RAY DIFFRACTION99
2.3677-2.40460.3571310.32381806X-RAY DIFFRACTION96
2.4046-2.4440.33821520.3141849X-RAY DIFFRACTION99
2.444-2.48610.34091370.30251797X-RAY DIFFRACTION97
2.4861-2.53130.38191470.3031816X-RAY DIFFRACTION98
2.5313-2.57990.34151320.29971794X-RAY DIFFRACTION95
2.5799-2.63250.34361350.29181766X-RAY DIFFRACTION96
2.6325-2.68970.33111450.27731861X-RAY DIFFRACTION100
2.6897-2.75220.33141660.27821766X-RAY DIFFRACTION97
2.7522-2.82090.30841260.27131895X-RAY DIFFRACTION100
2.8209-2.89710.28141280.26251804X-RAY DIFFRACTION97
2.8971-2.98220.34381590.26451860X-RAY DIFFRACTION99
2.9822-3.07830.26171360.25551780X-RAY DIFFRACTION97
3.0783-3.18810.31631270.25951798X-RAY DIFFRACTION96
3.1881-3.31550.27041500.23711874X-RAY DIFFRACTION99
3.3155-3.4660.25791350.22561820X-RAY DIFFRACTION98
3.466-3.64820.25311410.22721858X-RAY DIFFRACTION98
3.6482-3.8760.22671410.21981811X-RAY DIFFRACTION98
3.876-4.1740.2831260.21961857X-RAY DIFFRACTION97
4.174-4.59170.2521350.19241817X-RAY DIFFRACTION99
4.5917-5.25070.22781410.19431848X-RAY DIFFRACTION99
5.2507-6.59510.25941420.25841833X-RAY DIFFRACTION98
6.5951-24.95840.21951470.23661806X-RAY DIFFRACTION97

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