+
Open data
-
Basic information
Entry | Database: PDB / ID: 5djt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of LOV2 (C450A) domain in complex with Zdk2 | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / Protein binding / Protein engineering / Photoswitch / Light-induced signal transduction / LOV2 / Affibody / Complex | ||||||
Function / homology | ![]() blue light photoreceptor activity / protein kinase activity / protein phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tarnawski, M. / Wang, H. / Yumerefendi, H. / Hahn, K.M. / Schlichting, I. | ||||||
![]() | ![]() Title: LOVTRAP: an optogenetic system for photoinduced protein dissociation. Authors: Wang, H. / Vilela, M. / Winkler, A. / Tarnawski, M. / Schlichting, I. / Yumerefendi, H. / Kuhlman, B. / Liu, R. / Danuser, G. / Hahn, K.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 105.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 79.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 746.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 747.1 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5djuC ![]() 5efwC ![]() 2kzjS ![]() 2wkqS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 16631.729 Da / Num. of mol.: 1 / Fragment: UNP residues 404-546 / Mutation: C450A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 6674.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 279 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / |
---|---|
#4: Chemical | ChemComp-FMN / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M tri-sodium citrate pH 5.6, 0.2 M ammonium acetate, 32% (w/v) PEG 4000 and 0.1 M copper(II) chloride as an additive |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00005 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 44465 / % possible obs: 99.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2WKQ and a homology model based on 2KZJ Resolution: 1.4→35.507 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 14.69 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→35.507 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|