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- PDB-4x9w: PLK-1 polo-box domain in complex with Bioactive Imidazolium-conta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x9w | |||||||||
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Title | PLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide macrocycle 4C | |||||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | ![]() Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Grant, R.A. / Qian, W.-J. / Yaffe, M.B. / Burke, T.R. | |||||||||
![]() | ![]() Title: Neighbor-directed histidine N ( tau )-alkylation: A route to imidazolium-containing phosphopeptide macrocycles. Authors: Qian, W.J. / Park, J.E. / Grant, R. / Lai, C.C. / Kelley, J.A. / Yaffe, M.B. / Lee, K.S. / Burke, T.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4x9rC ![]() 4x9vC ![]() 3rq7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27285.158 Da / Num. of mol.: 1 / Fragment: POLO box domain residues 371-603 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 909.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.02 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion / pH: 8 Details: Frozen stocks of protein at 37 mg/mL in 10 mM TRIS pH8, 0.5 M NaCl, 10 mM DTT were thawed and diluted to 10 mg/ml with the same buffer. Complexes with each of three macrocycle compounds (3b, ...Details: Frozen stocks of protein at 37 mg/mL in 10 mM TRIS pH8, 0.5 M NaCl, 10 mM DTT were thawed and diluted to 10 mg/ml with the same buffer. Complexes with each of three macrocycle compounds (3b, 3c and 4b) were prepared by adding 100 mM stocks of the macrocycle in DMSO directly to the diluted protein to achieve a final concentration of 1 mM. Crystals were grown by hanging drop vapor diffusion, with drops made by mixing equal volumes of protein-macrocycle complex and well solution containing 2-6% PEG-3350. Crystals were cryo-protected by quickly dipping in a solution of 37.5% ethylene glycol in well solution and frozen in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.798→100 Å / Num. obs: 18528 / % possible obs: 95.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 27.05 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 1.153 / Net I/av σ(I): 32.875 / Net I/σ(I): 7 / Num. measured all: 117363 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3RQ7 Resolution: 1.798→38.065 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.798→38.065 Å
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Refine LS restraints |
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LS refinement shell |
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