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Yorodumi- PDB-7ko6: C1B domain of Protein kinase C in complex with ingenol-3-angelate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ko6 | ||||||
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Title | C1B domain of Protein kinase C in complex with ingenol-3-angelate and phosphocholine | ||||||
Components | Protein kinase C delta type | ||||||
Keywords | LIPID BINDING PROTEIN / C1 / lipid-binding / diacylglycerol-binding / Zn2+ finger | ||||||
Function / homology | Function and homology information protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / regulation of metabolic process / response to stimulus / cell cycle / phosphorylation / apoptotic process / perinuclear region of cytoplasm / ATP binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Katti, S.S. / Krieger, I.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists. Authors: Katti, S.S. / Krieger, I.V. / Ann, J. / Lee, J. / Sacchettini, J.C. / Igumenova, T.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ko6.cif.gz | 29.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ko6.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ko6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/7ko6 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/7ko6 | HTTPS FTP |
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-Related structure data
Related structure data | 7kndC 7knjC 7l92C 7lcbC 7leoC 7lf3C 1ptqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6097.217 Da / Num. of mol.: 1 / Fragment: C1B domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkcd, rCG_42255 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140UHX0, protein kinase C | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-WUD / | #4: Chemical | ChemComp-XP5 / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.04 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Screen condition: 0.2 M Ammonium acetate, 0.1 M Sodium phosphate, 30% Isopropanol, pH 6.8, Drop condition: Protein: 2 mM in MES pH 6.5, 150 mM KCl, Phosphatidylcholine: 20 mM, Ingenol-3-angelate: 2.5 mM |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Sep 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→57 Å / Num. obs: 4819 / % possible obs: 100 % / Redundancy: 12.54 % / Rmerge(I) obs: 0.1144 / Net I/σ(I): 15.76 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.79 / Num. unique obs: 704 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ptq Resolution: 1.8→28.56 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.67 / 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 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 65 Å2 / Biso mean: 18.5386 Å2 / Biso min: 6.01 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→28.56 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %
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