[English] 日本語
![](img/lk-miru.gif)
- PDB-6rum: Crystal structure of GFP-LAMA-G97 - a GFP enhancer nanobody with ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6rum | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of GFP-LAMA-G97 - a GFP enhancer nanobody with cpDHFR insertion and TMP and NADPH | ||||||
![]() | GFP-LAMA-G97 a GFP enhancer nanobody with cpDHFR insertion | ||||||
![]() | PROTEIN BINDING / LAMA / nanobody / circular permutant of DHFR / TMP / NADPH | ||||||
Function / homology | ![]() methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Farrants, H. / Tarnawski, M. / Mueller, T.G. / Otsuka, S. / Hiblot, J. / Koch, B. / Kueblbeck, M. / Kraeusslich, H.-G. / Ellenberg, J. / Johnsson, K. | ||||||
![]() | ![]() Title: Chemogenetic Control of Nanobodies. Authors: Farrants, H. / Tarnawski, M. / Muller, T.G. / Otsuka, S. / Hiblot, J. / Koch, B. / Kueblbeck, M. / Krausslich, H.G. / Ellenberg, J. / Johnsson, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rulC ![]() 5h8dS ![]() 5uiiS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Antibody , 1 types, 1 molecules A
#1: Antibody | Mass: 30984.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Gene: folA, tmrA, b0048, JW0047 / Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 302 molecules ![](data/chem/img/TOP.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-TOP / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-NDP / | ||||||
#4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M MES pH 6.0, 20% (w/v) PEG 6000, 1.0 M lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 37239 / % possible obs: 99.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.23 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 6123 / % possible all: 98.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5UII, 5H8D Resolution: 1.6→47.715 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.47
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→47.715 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|