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Yorodumi- PDB-1gpo: CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FA... -
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-Basic information
Entry | Database: PDB / ID: 1gpo | ||||||
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Title | CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT | ||||||
Components | (ANTIBODY M41) x 2 | ||||||
Keywords | IMMUNE SYSTEM / PROTEIN ENGINEERING / ANTIBODY DESIGN / IMMUNOGLOBULIN STRUCTURE / ANTIGEN-BINDING SITE / CANONICAL CONFORMATION / COMPLEMENTARITY-DETERMINING REGION | ||||||
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 / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Schiweck, W. / Skerra, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: The rational construction of an antibody against cystatin: lessons from the crystal structure of an artificial Fab fragment. Authors: Schiweck, W. / Skerra, A. #1: Journal: Proteins / Year: 1995 Title: Fermenter Production of an Artificial Fab Fragment, Rationally Designed for the Antigen Cystatin, and its Optimized Crystallization Through Constant Domain Shuffling Authors: Schiweck, W. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gpo.cif.gz | 191.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gpo.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gpo ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gpo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.997725, 0.020407, -0.064249), Vector: |
-Components
#1: Antibody | Mass: 24172.518 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PASK85-M41 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 W3110 / References: UniProt: P01837 #2: Antibody | Mass: 24182.809 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PASK85-M41 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 W3110 / References: EMBL: AJ303449, UniProt: P01868*PLUS #3: Chemical | #4: 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: 2.94 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 2.0 M AMMONIUM SULFATE, 5 % DMSO, 0.1 M CACODYLATE PH 6.5 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting dropDetails: Schiweck, W., (1995) Proteins: Struct.,Funct., Genet., 23, 561. | ||||||||||||||||||||
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: Mar 1, 1995 |
Radiation | Monochromator: NICKEL FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→60 Å / Num. obs: 69136 / % possible obs: 84.6 % / Observed criterion σ(I): 0.5 / Redundancy: 2.6 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.215 / % possible all: 50.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HYBRID FAB FRAGMENT CONSISTING OF THE MODELLED STRUCTURE FOR THE ARTIFICIAL FV FRAGMENT M41 AND CONSTANT DOMAINS OF THE ANTI-LYSOZYME ANTIBODY HYHEL-10 Resolution: 1.95→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 28.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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