[English] 日本語
![](img/lk-miru.gif)
- PDB-4kuz: Crystal structure of anti-emmprin antibody 4A5 Fab in trigonal form -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4kuz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of anti-emmprin antibody 4A5 Fab in trigonal form | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / immunoglobulin fold | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Teplyakov, A. / Obmolova, G. / Gilliland, G.L. | ||||||
![]() | ![]() Title: Structural evidence for a constrained conformation of short CDR-L3 in antibodies. Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Gilliland, G.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 97.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 455.6 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kq3C ![]() 1igjS ![]() 1il1S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 24103.822 Da / Num. of mol.: 1 Fragment: Fab (mouse variable domain, human constant domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK293E / Production host: ![]() | ||
---|---|---|---|
#2: Antibody | Mass: 24591.381 Da / Num. of mol.: 1 Fragment: Fab (mouse variable domain, human constant domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK293E / Production host: ![]() | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 73.28 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1 M CHES, pH 9.5, 2.0 M ammonium sulfate, 5% isopropanol, cryoprotectant: mother liquor + 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 24, 2008 / Details: VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 24553 / Num. obs: 24553 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4 / % possible all: 93 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1IL1 AND 1IGJ Resolution: 2.7→29.2 Å / Cor.coef. Fo:Fc: 0.832 / Cor.coef. Fo:Fc free: 0.764 / σ(F): 1.34 / Phase error: 33.96 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.1 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.2 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|