+Open data
-Basic information
Entry | Database: PDB / ID: 2r23 | |||||||||
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Title | Crystal structure of S25-2 Fab in complex with Kdo analogues | |||||||||
Components | (Fab, antibody fragment (IgG1k), ...) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / Fab / anti-carbohydrate antibody | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | |||||||||
Authors | Brooks, C.L. / Evans, S.V. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes. Authors: Brooks, C.L. / Muller-Loennies, S. / 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 | 2r23.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r23.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 2r23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r23_validation.pdf.gz | 820.1 KB | Display | wwPDB validaton report |
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Full document | 2r23_full_validation.pdf.gz | 832.5 KB | Display | |
Data in XML | 2r23_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 2r23_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/2r23 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/2r23 | HTTPS FTP |
-Related structure data
Related structure data | 2r1wC 2r1xC 2r1yC 2r2bC 2r2eC 2r2hC 3bpcC 1q9q 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: 24242.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q52L64*PLUS |
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#2: Antibody | Mass: 24329.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) |
-Sugars , 1 types, 1 molecules
#3: Polysaccharide | D-glycero-alpha-D-talo-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2- ...D-glycero-alpha-D-talo-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid Type: oligosaccharide / Mass: 514.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 373 molecules
#4: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-ZN / |
#6: 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: 50.91 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, ethelyene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 8, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→19.9 Å / Num. obs: 57118 / % possible obs: 95.8 % / Redundancy: 4.42 % / Rmerge(I) obs: 0.044 / Χ2: 0.94 / Net I/σ(I): 13.5 / Scaling rejects: 1907 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 1Q9Q 1q9q Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.622 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.178 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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