+Open data
-Basic information
Entry | Database: PDB / ID: 1ncw | ||||||
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Title | Cationic Cyclization Antibody 4C6 in Complex with Benzoic Acid | ||||||
Components | (IMMUNOGLOBULIN IGG2A) x 2 | ||||||
Keywords | IMMUNE SYSTEM / immunoglobulin / catalytic antibody / cationic cyclization reaction | ||||||
Function / homology | Function and homology information positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment ...positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / multivesicular body / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular space / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Zhu, X. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction Authors: Zhu, X. / Heine, A. / Monnat, F. / Houk, K.N. / Janda, K.D. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ncw.cif.gz | 209 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ncw.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ncw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1ncw ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1ncw | HTTPS FTP |
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-Related structure data
Related structure data | 1nd0C 1mrdS 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 24219.010 Da / Num. of mol.: 1 / Fragment: Antibody FAB fragment 4C6, light chain / Source method: isolated from a natural source / Details: PURIFIED FROM ASCITIC FLUID / Source: (natural) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: Q58EU8*PLUS | ||||
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#2: Antibody | Mass: 23816.590 Da / Num. of mol.: 1 / Fragment: Antibody FAB fragment 4C6, heavy chain / Source method: isolated from a natural source / Details: PURIFIED FROM ASCITIC FLUID / Source: (natural) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: P01865*PLUS | ||||
#3: Chemical | ChemComp-BEZ / | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | AN APPROPRIAT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.66 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 5.6 Details: PEG4000, ammonium acetate, tri-sodium citrate, pH 5.6, Evaporation, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2000 |
Radiation | Monochromator: Double cyrstal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 137097 / Num. obs: 117957 / % possible obs: 86 % / Observed criterion σ(F): 0 / Redundancy: 3.85 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.5 / % possible all: 69.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 3.9 % |
Reflection shell | *PLUS % possible obs: 69.6 % / Num. unique obs: 4684 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MRD Resolution: 1.3→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Initial refinement begun with CNS
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Num. reflection Rfree: 7132 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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