+Open data
-Basic information
Entry | Database: PDB / ID: 1bm3 | ||||||
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Title | IMMUNOGLOBULIN OPG2 FAB-PEPTIDE COMPLEX | ||||||
Components |
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Keywords | IMMUNE SYSTEM / 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 / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis ...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 / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kodandapani, R. / Veerapandian, L. / Ni, C.Z. / Chiou, C.-K. / Whital, R. / Kunicki, T.J. / Ely, K.R. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 1998 Title: Conformational change in an anti-integrin antibody: structure of OPG2 Fab bound to a beta 3 peptide. Authors: Kodandapani, R. / Veerapandian, L. / Ni, C.Z. / Chiou, C.K. / Whittal, R.M. / Kunicki, T.J. / Ely, K.R. #1: Journal: J.Biol.Chem. / Year: 1995 Title: Crystal structure of the OPG2 Fab. An antireceptor antibody that mimics an RGD cell adhesion site. Authors: Kodandapani, R. / Veerapandian, B. / Kunicki, T.J. / Ely, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bm3.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bm3.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bm3_validation.pdf.gz | 430.2 KB | Display | wwPDB validaton report |
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Full document | 1bm3_full_validation.pdf.gz | 478.2 KB | Display | |
Data in XML | 1bm3_validation.xml.gz | 27 KB | Display | |
Data in CIF | 1bm3_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/1bm3 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/1bm3 | HTTPS FTP |
-Related structure data
Related structure data | 1opgS 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
#1: Antibody | Mass: 23549.811 Da / Num. of mol.: 1 / Fragment: CONSTANT DOMAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 24508.473 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868*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: 2.44 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 0.1M CACODYLATE, PH6.5, 0.2M CALCIUM ACETATE AND 16% PEG 8000 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Mar 12, 1992 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 20334 / % possible obs: 78 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.044 / Rsym value: 0.054 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OPG Resolution: 2→8 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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