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- PDB-7leo: C1B domain of Protein kinase C in complex with diacylglycerol-lac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7leo | ||||||
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Title | C1B domain of Protein kinase C in complex with diacylglycerol-lactone (AJH-836) and 1,2-diheptanoyl-sn-glycero-3-phosphocholine | ||||||
![]() | Protein kinase C delta type | ||||||
![]() | LIPID BINDING PROTEIN / C1 / lipid-binding / diacylglycerol-binding / Zn2+ finger | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Katti, S.S. / Krieger, I. | ||||||
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 | ![]() | 43 KB | Display | ![]() |
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PDB format | ![]() | 27.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kndC ![]() 7knjC ![]() 7ko6C ![]() 7l92C ![]() 7lcbC ![]() 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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2 | ![]()
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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.: 2 / Fragment: C1B domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-XZJ / {( | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.4 % |
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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 condition: Protein 2 mM in MES pH 6.5, 150 mM KCl; Phosphatidylcholine: 20 mM; AJH-836: 2.2 mM |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.64→50 Å / Num. obs: 17721 / % possible obs: 98.5 % / Redundancy: 5.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.049 / Rrim(I) all: 0.116 / Χ2: 2.096 / Net I/σ(I): 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1ptq Resolution: 1.65→29.96 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.32 / 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: 70.03 Å2 / Biso mean: 36.7592 Å2 / Biso min: 20.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→29.96 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: 6
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