+Open data
-Basic information
Entry | Database: PDB / ID: 1opg | ||||||
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Title | OPG2 FAB FRAGMENT | ||||||
Components |
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Keywords | IMMUNOGLOBULIN / CELL ADHESION MOLECULE | ||||||
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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Kodandapani, R. / Veerapandian, B. / Ely, K.R. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1992 Title: Crystallization of Opg2 Fab Fragment: A Fibrinogen Mimic with Specificity for the Platelet Glycoprotein Authors: Celikel, R. / Williamson, M.M. / 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 | 1opg.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1opg.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 1opg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1opg_validation.pdf.gz | 377.1 KB | Display | wwPDB validaton report |
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Full document | 1opg_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 1opg_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1opg_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/1opg ftp://data.pdbj.org/pub/pdb/validation_reports/op/1opg | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 / 4: CIS PROLINE - PRO H 159 / 5: CIS PROLINE - PRO H 161 |
-Components
#1: Antibody | Mass: 23549.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLATELET |
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#2: Antibody | Mass: 24508.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLATELET / References: UniProt: P01868 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging dropDetails: Celikel, R., (1993) Acta Crystallogr.,Sect.D, 49, 421. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Date: Mar 12, 1992 |
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Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 28703 / % possible obs: 99 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.044 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 89211 / Rmerge(I) obs: 0.044 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å / σ(F): 3 /
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Displacement parameters | Biso mean: 30.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |