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Open data
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Basic information
Entry | Database: PDB / ID: 8ojt | ||||||
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Title | Crystal structure of the human IgD Fab - structure Fab2 | ||||||
![]() | (Human IgD Fab ...) x 2 | ||||||
![]() | IMMUNE SYSTEM / Fab / Antibody / Immunoglobulin | ||||||
Function / homology | AZIDE ION / NITRATE ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Davies, A.M. / Beavil, R.L. / McDonnell, J.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of the human IgD Fab reveal insights into C H 1 domain diversity. Authors: Davies, A.M. / Beavil, R.L. / Barbolov, M. / Sandhar, B.S. / Gould, H.J. / Beavil, A.J. / Sutton, B.J. / McDonnell, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.5 KB | Display | ![]() |
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PDB format | ![]() | 155.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.8 KB | Display | ![]() |
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Full document | ![]() | 488.6 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ojsC ![]() 8ojuC ![]() 8ojvC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 22769.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 25399.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 6 types, 349 molecules ![](data/chem/img/NO3.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M BTP pH 6.5, 20% PEG 3350 and 0.2M sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→70.39 Å / Num. obs: 64083 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 18.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3165 / CC1/2: 0.486 / Rpim(I) all: 0.923 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→70.39 Å
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Refine LS restraints |
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LS refinement shell |
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