+
Open data
-
Basic information
Entry | Database: PDB / ID: 5i1k | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV3-20 | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / MONOCLONAL ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Teplyakov, A. / Obmolova, G. / Malia, T. / Luo, J. / Gilliland, G. | ||||||
![]() | ![]() Title: Structural diversity in a human antibody germline library. Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Muzammil, S. / Sweet, R. / Almagro, J.C. / Gilliland, G.L. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 Title: Protein crystallization with microseed matrix screening: application to human germline antibody Fabs. Authors: Obmolova, G. / Malia, T.J. / Teplyakov, A. / Sweet, R.W. / Gilliland, G.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 106.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.7 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i15C ![]() 5i16C ![]() 5i17C ![]() 5i18C ![]() 5i19C ![]() 5i1aC ![]() 5i1cC ![]() 5i1dC ![]() 5i1eC ![]() 5i1gC ![]() 5i1hC ![]() 5i1iC ![]() 5i1jC ![]() 5i1lC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23373.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Antibody | Mass: 24544.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 4 types, 537 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NHE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NHE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-NHE / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 1.0 M AMMONIUM SULFATE, 0.1 M CHES PH 9.5 / PH range: 9.5 |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 18, 2009 / 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: 1.65→28.2 Å / Num. obs: 53058 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.65→1.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 5.8 / % possible all: 49.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|