[English] 日本語
Yorodumi- PDB-7knj: C1B domain of Protein kinase C in complex with Phorbol ester and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7knj | ||||||
---|---|---|---|---|---|---|---|
Title | C1B domain of Protein kinase C in complex with Phorbol ester and Phosphatidylcholine | ||||||
Components | Protein kinase C delta type | ||||||
Keywords | LIPID BINDING PROTEIN / C1 / lipid-binding / phorbol ester 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: 1.57 Å | ||||||
Authors | Katti, S.S. / Krieger, I. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7knj.cif.gz | 30.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7knj.ent.gz | 17 KB | Display | PDB format |
PDBx/mmJSON format | 7knj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/7knj ftp://data.pdbj.org/pub/pdb/validation_reports/kn/7knj | HTTPS FTP |
---|
-Related structure data
Related structure data | 7kndC 7ko6C 7l92C 7lcbC 7leoC 7lf3C 1ptqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-WTS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.88 % |
---|---|
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, Phorbol ester: 2.5 mM |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Sep 5, 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: 1.57→57.7 Å / Num. obs: 6195 / % possible obs: 85 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.0548 / Net I/σ(I): 21.05 |
Reflection shell | Resolution: 1.57→1.67 Å / Redundancy: 0.44 % / Rmerge(I) obs: 0.2054 / Num. possible: 1217 / Num. unique obs: 414 / % possible all: 34 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ptq Resolution: 1.57→19.24 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 23.91 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 82.57 Å2 / Biso mean: 19.1568 Å2 / Biso min: 4.97 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.57→19.24 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
|