[English] 日本語
![](img/lk-miru.gif)
- PDB-8cge: The crystal structure of a cobalt-bound scFv reveals a Tetrameric... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8cge | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a cobalt-bound scFv reveals a Tetrameric polyHistidine motif (TetrHis) | ||||||
![]() | Single Chain Fv 2A2 | ||||||
![]() | METAL BINDING PROTEIN / Single Chain Fragment Variable Antibody / tetrameric polyhistidine TetrHis motif / cobalt-bound | ||||||
Function / homology | : ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Healey, R.D. / Hoh, F. / Granier, S. / Leyrat, C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure, dynamics and transferability of the metal-dependent polyhistidine tetramerization motif TetrHis for single-chain Fv antibodies. Authors: Healey, R.D. / Couillaud, L. / Hoh, F. / Mouhand, A. / Fouillen, A. / Couvineau, P. / Granier, S. / Leyrat, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 257.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 174.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.586115834054, 0.369218282168, 0.721211542603), (0.169450102625, -0.81459115152, 0.554732294522), (0.792309845825, 0.447346751389, 0.414880696381)Vector: -3. ...NCS oper: (Code: given Matrix: (-0.586115834054, 0.369218282168, 0.721211542603), Vector: |
-
Components
#1: Antibody | Mass: 32311.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Cell line (production host): S2 / Production host: ![]() ![]() #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CXS / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.52 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.01M cobalt chloride, 0.1M MES, pH6.5, 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.47 Å / Num. obs: 28177 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 44.77 Å2 / CC1/2: 0.989 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.5→2.6 Å / Num. unique obs: 635 / CC1/2: 0.491 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.17 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 6.03782312577 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -11.6715415952 Å / Origin y: -15.1313179124 Å / Origin z: -11.1290017382 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|