+Open data
-Basic information
Entry | Database: PDB / ID: 1lo4 | ||||||
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Title | Retro-Diels-Alderase Catalytic antibody 9D9 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / catalytic antibody / retro-Deils-Alderase | ||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / immune response / extracellular space / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hugot, M. / Reymond, J.L. / Baumann, U. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue. Authors: Hugot, M. / Bensel, N. / Vogel, M. / Reymond, M.T. / Stadler, B. / Reymond, J.L. / Baumann, U. | ||||||
History |
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Remark 999 | At the time of processing, this sequence has not yet been deposited in a sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lo4.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lo4.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1lo4 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1lo4 | HTTPS FTP |
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-Related 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: 23994.537 Da / Num. of mol.: 1 / Fragment: Fab fragment / Source method: isolated from a natural source Details: The antibodies were isolated from hybridoma cells and Fab fragments were generated by papain digestion. Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99M37, UniProt: Q65ZC0*PLUS |
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#2: Antibody | Mass: 23656.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The antibodies were isolated from hybridoma cells and Fab fragments were generated by papain digestion. Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91Z05*PLUS |
#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: 2.57 Å3/Da / Density % sol: 52.09 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG4000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 1999 / Details: Yale mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 19718 / % possible obs: 99 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 10.6 / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 40 Å / % possible obs: 99 % / Num. measured all: 182312 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 98.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.35 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.865 / SU B: 9.885 / SU ML: 9.885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.466 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.887 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→38.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.25 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.46 Å |