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- PDB-3d5w: Crystal structure of a phosphorylated Polo-like kinase 1 (Plk1) c... -

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Basic information

Entry
Database: PDB / ID: 3d5w
TitleCrystal structure of a phosphorylated Polo-like kinase 1 (Plk1) catalytic domain in complex with ADP.
ComponentsPolo-like kinase 1PLK1
KeywordsTRANSFERASE / Polo-like kinase 1 / Plk1 / catalytic domain / small-molecule inhibitor / Kinase
Function / homology
Function and homology information


polo kinase / mitotic spindle organization / kinetochore / spindle pole / retina development in camera-type eye / mitotic cell cycle / midbody / cell division / phosphorylation / protein serine/threonine kinase activity ...polo kinase / mitotic spindle organization / kinetochore / spindle pole / retina development in camera-type eye / mitotic cell cycle / midbody / cell division / phosphorylation / protein serine/threonine kinase activity / centrosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase PLK
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsElling, R.A. / Fucini, R.V. / Romanowski, M.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of the wild-type and activated catalytic domains of Brachydanio rerio Polo-like kinase 1 (Plk1): changes in the active-site conformation and interactions with ligands.
Authors: Elling, R.A. / Fucini, R.V. / Romanowski, M.J.
History
DepositionMay 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Polo-like kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4862
Polymers36,0591
Non-polymers4271
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.990, 133.990, 133.990
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 Polo-like kinase 1 / PLK1


Mass: 36058.949 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: plk1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q4KMI8, polo kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: hanging-drop vapor diffusion at 4 C (277K); protein at 6 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 3 mM DTT, 4 mM ATP, and 4 mM MgSO4; crystallization condition: 0.2 M disodium tartrate ...Details: hanging-drop vapor diffusion at 4 C (277K); protein at 6 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 3 mM DTT, 4 mM ATP, and 4 mM MgSO4; crystallization condition: 0.2 M disodium tartrate dihydrate and 20% PEG 3350; cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 6, 2006
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 12461 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3d5v

3d5v


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.282 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.7 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1113 8.9 %RANDOM
Rwork0.24155 ---
obs0.24418 11348 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.518 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 27 57 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222332
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.9943163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9545283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79522.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8891520
X-RAY DIFFRACTIONr_chiral_restr0.0580.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021737
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1620.21036
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21615
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1872.51463
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09852309
X-RAY DIFFRACTIONr_scbond_it0.8752.5972
X-RAY DIFFRACTIONr_scangle_it1.4465854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.691 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.434 108 -
Rwork0.326 1096 -
obs--99.92 %

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