+Open data
-Basic information
Entry | Database: PDB / ID: 4ods | ||||||
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Title | Unliganded Fab structure of lipid A-specific antibody S55-3 | ||||||
Components | (S55-3 Fab (IgG2b) heavy chain) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Carbohydrate binding | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||
Authors | Haji-Ghassemi, O. / Evans, S.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ods.cif.gz | 101.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ods.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ods.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ods_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 4ods_full_validation.pdf.gz | 438.1 KB | Display | |
Data in XML | 4ods_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 4ods_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/4ods ftp://data.pdbj.org/pub/pdb/validation_reports/od/4ods | HTTPS FTP |
-Related structure data
Related structure data | 4odtC 4oduC 4odvC 4odwC 4z8fC 4z95C 1nbvS 3s35S 4ody 4odz 4oe0 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23382.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
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#2: Antibody | Mass: 24105.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.97 % |
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Crystal grow | Temperature: 289 K / pH: 9.5 Details: Drop: 0.05M Glycine, 4% (w/v) PEG 3350 Reservoir: 24% (w/v) PEG 3350, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2011 / Details: OSMIC BLUE MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→79.39 Å / Num. obs: 33609 / % possible obs: 95.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.427 / % possible all: 92.2 |
-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FV FRAGMENT FROM PDB ENTRY 3S35, CONSTANT DOMAINS FROM PDB ENTRY 1NBV Resolution: 1.94→79.39 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.788 / SU ML: 0.133 / SU R Cruickshank DPI: 0.1889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.173 / 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: 27.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→79.39 Å
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Refine LS restraints |
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