+Open data
-Basic information
Entry | Database: PDB / ID: 3ijy | |||||||||
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Title | Structure of S67-27 in Complex with Kdo(2.8)Kdo | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / Kdo / Chlamydia / LPS / Fab / carbohydrate | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Brooks, C.L. / Blackler, R.J. / Evans, S.V. | |||||||||
Citation | Journal: Glycobiology / Year: 2010 Title: The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen. Authors: Brooks, C.L. / Blackler, R.J. / Sixta, G. / Kosma, P. / Muller-Loennies, S. / Brade, L. / Hirama, T. / Mackenzie, C.R. / 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 | 3ijy.cif.gz | 182.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ijy.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ijy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/3ijy ftp://data.pdbj.org/pub/pdb/validation_reports/ij/3ijy | HTTPS FTP |
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-Related structure data
Related structure data | 3ijhC 3ijsC 3ikcC 1q9wS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24079.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c #2: Antibody | Mass: 24530.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c #3: Polysaccharide | Type: oligosaccharide / Mass: 498.433 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 4, 2009 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→19.99 Å / Num. obs: 21232 / % possible obs: 95.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.107 / Χ2: 0.96 / Net I/σ(I): 7.6 / Scaling rejects: 2676 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1Q9W Resolution: 2.85→19.987 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 1.24 / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.345 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.38 Å2 / Biso mean: 45.102 Å2 / Biso min: 17.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→19.987 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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