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- PDB-7l92: C1B domain of Protein kinase C in complex with diacylglycerol and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l92 | ||||||
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Title | C1B domain of Protein kinase C in complex with diacylglycerol and dodecyl 2-(trimethylammonio)ethyl phosphate | ||||||
![]() | Protein kinase C delta type | ||||||
![]() | LIPID BINDING PROTEIN / C1 / lipid-binding / diacylglycerol-binding / Zn2+ finger | ||||||
Function / homology | ![]() protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / intracellular signal transduction / cell cycle / phosphorylation / apoptotic process / perinuclear region of cytoplasm / ATP binding / nucleus / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Katti, S.S. / Krieger, I.V. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.7 KB | Display | ![]() |
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PDB format | ![]() | 91.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.9 MB | Display | ![]() |
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Full document | ![]() | 4.1 MB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kndC ![]() 7knjC ![]() 7ko6C ![]() 7lcbC ![]() 7leoC ![]() 7lf3C ![]() 1ptqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 8 molecules ADGJMPSV
#1: Protein | Mass: 6097.217 Da / Num. of mol.: 8 / Fragment: C1B domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 265 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/DPV.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/DPV.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-DGA / #4: Chemical | #5: Chemical | ChemComp-DPV / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.06 % |
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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 15% Isopropanol pH 6.8 Drop conditions: For seed crystals Protein: 2 mM in MES pH 6.5, 150 mM KCl Dodecylphosphocholine: 20 mM ...Details: Screen condition: 0.2 M Ammonium acetate 0.1 M Sodium phosphate 15% Isopropanol pH 6.8 Drop conditions: For seed crystals Protein: 2 mM in MES pH 6.5, 150 mM KCl Dodecylphosphocholine: 20 mM 1,2-dioctanoyl-sn-glycerol: 2.5 mM Final drop Protein: 2 mM in MES pH 6.5, 150 mM KCl Dodecylphosphocholine: 10 mM 1,2-dioctanoyl-sn-glycerol: 2.5 mM |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→44.6 Å / Num. obs: 64618 / % possible obs: 99.1 % / Redundancy: 2.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.613 / Num. unique obs: 3574 / CC1/2: 0.528 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ptq Resolution: 1.75→28.96 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.28 / 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: 99.24 Å2 / Biso mean: 40.2307 Å2 / Biso min: 14.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→28.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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