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- PDB-4odt: Fab Structure of lipid A-specific antibody S1-15 in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4odt | |||||||||
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Title | Fab Structure of lipid A-specific antibody S1-15 in complex with lipid A carbohydrate backbone | |||||||||
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![]() | IMMUNE SYSTEM / Carbohydrate binding | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Haji-Ghassemi, O. / Evans, S.V. | |||||||||
![]() | ![]() Title: Structural Basis for Antibody Recognition of Lipid A: INSIGHTS TO POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA. Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Rodriguez, T. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.1 KB | Display | ![]() |
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PDB format | ![]() | 79.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.7 KB | Display | ![]() |
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Full document | ![]() | 782.2 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4odsSC ![]() 4oduC ![]() 4odvC ![]() 4odwC ![]() 4z8fC ![]() 4z95C ![]() 4ody ![]() 4odz ![]() 4oe0 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 on special symmetry positions |
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Components
#1: Antibody | Mass: 24349.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#2: Antibody | Mass: 23727.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
#3: Polysaccharide | 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Chemical | ChemComp-PG0 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 289 K / pH: 9 Details: 0.1M NaCl, 0.1M Bicine, and 30% (w/v) PEG 550 MME, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2011 / Details: VERTICAL FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→69.4 Å / Num. obs: 35405 / % possible obs: 100 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 15.8 % / Rmerge(I) obs: 0.786 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4ODS Resolution: 1.95→69.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.389 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1745 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→69.4 Å
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Refine LS restraints |
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