+Open data
-Basic information
Entry | Database: PDB / ID: 1kem | ||||||
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Title | CATALYTIC ANTIBODY 28B4 FAB FRAGMENT | ||||||
Components | (28B4 FAB) x 2 | ||||||
Keywords | CATALYTIC ANTIBODY / SULFIDE OXIDATION / MONOOXYGENASE / OXYGENATION / FAB / IMMUNOGLOBULIN | ||||||
Function / homology | Function and homology information humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Hsieh-Wilson, L.C. / Schultz, P.G. / Stevens, R.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution. Authors: Hsieh-Wilson, L.C. / Schultz, P.G. / Stevens, R.C. #1: Journal: J.Am.Chem.Soc. / Year: 1994 Title: An Efficient Antibody-Catalyzed Monooxygenation Reaction Authors: Hsieh, L.C. / Stephans, J.C. / Schultz, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kem.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kem.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/1kem ftp://data.pdbj.org/pub/pdb/validation_reports/ke/1kem | 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: 23994.625 Da / Num. of mol.: 1 / Fragment: VARIABLE REGIONS OF LIGHT AND HEAVY CHAINS / Source method: isolated from a natural source Details: THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ANTIBODY BY PAPAIN Source: (natural) Mus musculus (house mouse) / Cell line: 28B4 / Strain: BALB/C / References: PIR: PC4203 |
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#2: Antibody | Mass: 23391.201 Da / Num. of mol.: 1 / Fragment: VARIABLE REGIONS OF LIGHT AND HEAVY CHAINS / Source method: isolated from a natural source Details: THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ANTIBODY BY PAPAIN Source: (natural) Mus musculus (house mouse) / Cell line: 28B4 / Strain: BALB/C / References: UniProt: P01868 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 21852 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.078 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 8 / % possible all: 43 |
Reflection | *PLUS Num. measured all: 51820 |
Reflection shell | *PLUS % possible obs: 43 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / σ(F): 0 Details: RESIDUES SER H 126 - ALA H 135 DISPLAYED WEAK ELECTRON DENSITY AND ARE CONSIDERED DISORDERED IN THIS STRUCTURE.
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |