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- PDB-3i9g: Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i9g | ||||||
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Title | Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragment in complex with sphingosine-1-phosphate | ||||||
![]() | (Sonepcizumab antibody Fab fragment, ...) x 2 | ||||||
![]() | IMMUNE SYSTEM / Antibody / Fab / Sphingosine-1-phosphate / Calcium / Immunoglobin / IgG | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-S1P![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Huxford, T. | ||||||
![]() | ![]() Title: The crystal structure of sphingosine-1-phosphate in complex with a Fab fragment reveals metal bridging of an antibody and its antigen. Authors: Wojciak, J.M. / Zhu, N. / Schuerenberg, K.T. / Moreno, K. / Shestowsky, W.S. / Hiraiwa, M. / Sabbadini, R. / Huxford, T. #1: Journal: J.Lipid Res. / Year: 2009 Title: Production and characterization of monoclonal anti-sphingosine-1-phosphate antibodies Authors: O'Brien, N. / Jones, S.T. / Williams, D.G. / Cunningham, H.B. / Moreno, K. / Visentin, B. / Gentile, A. / Vekich, J. / Shestowsky, W. / Hiraiwa, M. / Matteo, R. / Cavalli, A. / Grotjahn, D. ...Authors: O'Brien, N. / Jones, S.T. / Williams, D.G. / Cunningham, H.B. / Moreno, K. / Visentin, B. / Gentile, A. / Vekich, J. / Shestowsky, W. / Hiraiwa, M. / Matteo, R. / Cavalli, A. / Grotjahn, D. / Grant, M. / Hansen, G. / Campbell, M.A. / Sabbadini, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.9 KB | Display | ![]() |
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PDB format | ![]() | 81.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24027.127 Da / Num. of mol.: 1 / Fragment: Fab Fragment Source method: isolated from a genetically manipulated source Details: Humanized mouse IgG1K expressed from a stable transfected CHO cell line Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23442.965 Da / Num. of mol.: 1 / Fragment: Fab Fragment Source method: isolated from a genetically manipulated source Details: Humanized mouse IgG1K expressed from a stable transfected CHO cell line Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 291 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/S1P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/S1P.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-S1P / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.04 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1 microliter of 12 mg/mL S1P:Fab complex was mixed with 1 microliter and sealed over 1 mL of reservoir solution containing 22% (w/v) polyethylene glycol 3350, 100 mM MgSO4, 100 mM sodium ...Details: 1 microliter of 12 mg/mL S1P:Fab complex was mixed with 1 microliter and sealed over 1 mL of reservoir solution containing 22% (w/v) polyethylene glycol 3350, 100 mM MgSO4, 100 mM sodium citrate (pH 6.0) and 10% (v/v) ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 21, 2008 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 52056 / Num. obs: 50494 / % possible obs: 97 % / Observed criterion σ(I): 3.8 / Redundancy: 5.1 % / Rsym value: 0.055 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.18 / Num. unique all: 3940 / Rsym value: 0.409 / % possible all: 76.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.32 Å2 / Biso mean: 28.232 Å2 / Biso min: 14.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.951 Å / Total num. of bins used: 20
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