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Yorodumi- PDB-9cmz: Crystal Structure of Cdk-related protein kinase 6 (PK6) from Plas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cmz | |||||||||
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Title | Crystal Structure of Cdk-related protein kinase 6 (PK6) from Plasmodium falciparum in complex with inhibitor KG2-051 | |||||||||
Components | Protein kinase 6 | |||||||||
Keywords | TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Protein kinase 6 / Plasmodium falciparum / inhibitor | |||||||||
Function / homology | Function and homology information mediator complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / protein phosphorylation / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal Structure of Cdk-related protein kinase 6 (PK6) from Plasmodium falciparum in complex with inhibitor KG2-051 Authors: Seibold, S. / Lovell, S. / Mian, M.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cmz.cif.gz | 353.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cmz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9cmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cmz_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 9cmz_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 9cmz_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 9cmz_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/9cmz ftp://data.pdbj.org/pub/pdb/validation_reports/cm/9cmz | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35847.383 Da / Num. of mol.: 3 / Mutation: C44N, C53R, C222N, K237A, K86A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1337100 / Plasmid: PlfaA.01252.a.A13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8IDW1, cyclin-dependent kinase #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | Mass: 502.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H25Cl2N5OS / Feature type: SUBJECT OF INVESTIGATION #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Berkeley F7: 20% (w/v) PEG MME 5000, 100 mM Tris pH 8.5, 200 mM lithium sulfate. PlfaA.01252.a.A13.PW39218 at 15.9 mg/mL. His tag cleaved with 3C protease. 2mM KG2-051 added prior to ...Details: Berkeley F7: 20% (w/v) PEG MME 5000, 100 mM Tris pH 8.5, 200 mM lithium sulfate. PlfaA.01252.a.A13.PW39218 at 15.9 mg/mL. His tag cleaved with 3C protease. 2mM KG2-051 added prior to crystallization. plate SS CloverBook4_pg5, Cryo: 80% crystallant + 20% PEG200. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: May 30, 2024 |
Radiation | Monochromator: HELIOS MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→44.4 Å / Num. obs: 42580 / % possible obs: 99.3 % / Redundancy: 11.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.037 / Rrim(I) all: 0.127 / Χ2: 1.13 / Net I/σ(I): 18.8 / Num. measured all: 494144 |
Reflection shell | Resolution: 2.45→2.54 Å / % possible obs: 99.6 % / Redundancy: 10.3 % / Rmerge(I) obs: 1.894 / Num. measured all: 45821 / Num. unique obs: 4470 / CC1/2: 0.698 / Rpim(I) all: 0.602 / Rrim(I) all: 1.99 / Χ2: 0.93 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→34.66 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→34.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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