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Yorodumi- PDB-3i02: Crystal structure of S54-10 antibody in complex with antigen Kdo(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i02 | |||||||||
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Title | Crystal structure of S54-10 antibody in complex with antigen Kdo(2.4)Kdo(2.4)Kdo | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / Fab / IgG / 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 / molecular replacement / Resolution: 2.6 Å | |||||||||
Authors | Brooks, C.L. / Muller-Loennies, S. / Borisova, S.N. / Brade, L. / Kosma, P. / Hirama, T. / MacKenzie, C.R. / Brade, H. / Evans, S.V. | |||||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Antibodies raised against chlamydial lipopolysaccharide antigens reveal convergence in germline gene usage and differential epitope recognition Authors: Brooks, C.L. / Muller-Loennies, S. / Borisova, S.N. / Brade, L. / Kosma, P. / 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 | 3i02.cif.gz | 182.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i02.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 3i02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/3i02 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/3i02 | HTTPS FTP |
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-Related structure data
Related structure data | 3hzkC 3hzmC 3hzvC 3hzyC 1q9t 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: 24327.041 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: 24293.379 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: 718.610 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #4: 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: 2.48 Å3/Da / Density % sol: 50.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 14, 2007 / Details: Osmic Blue | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→19.99 Å / Num. obs: 28890 / % possible obs: 97.3 % / Redundancy: 3.69 % / Rmerge(I) obs: 0.097 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Q9T 1q9t Resolution: 2.6→19.99 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.96 / σ(F): 1.36 / Phase error: 27.67 / 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: 42.716 Å2 / ksol: 0.372 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.257 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.99 Å
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Refine LS restraints |
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LS refinement shell |
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