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Yorodumi- PDB-3hzk: Crystal structure of S73-2 antibody in complex with antigen Kdo(2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hzk | |||||||||
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Title | Crystal structure of S73-2 antibody in complex with antigen Kdo(2.4)Kdo | |||||||||
Components | (S73-2 Fab (IgG1k) ...) x 2 | |||||||||
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: 2.15 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 | 3hzk.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hzk.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 3hzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/3hzk ftp://data.pdbj.org/pub/pdb/validation_reports/hz/3hzk | HTTPS FTP |
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-Related structure data
Related structure data | 3hzmC 3hzvC 3hzyC 3i02C 1q9r 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
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 24213.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
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#2: Antibody | Mass: 24448.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
-Sugars , 1 types, 1 molecules
#3: Polysaccharide | 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid Type: oligosaccharide / Mass: 498.433 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 169 molecules
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: 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: 2.47 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, Ethylene glycol, ZnCl2, MgCl2, pH 8.0, 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: Nov 24, 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: 2.15→19.86 Å / Num. obs: 25575 / % possible obs: 94.9 % / Redundancy: 4.73 % / Rmerge(I) obs: 0.061 / Χ2: 0.99 / Scaling rejects: 915 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 32.89 / 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 1Q9R 1q9r Resolution: 2.15→19.752 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.778 / SU ML: 0.22 / 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: 43.193 Å2 / ksol: 0.384 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.78 Å2 / Biso mean: 34.031 Å2 / Biso min: 17.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→19.752 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: 9
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