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Open data
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Basic information
Entry | Database: PDB / ID: 1l7t | ||||||
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Title | Crystal Structure Analysis of the anti-testosterone Fab fragment | ||||||
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![]() | IMMUNE SYSTEM / anti-testosterone / fab fragment / affinity and specificity matured | ||||||
Function / homology | ![]() Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / 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 / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / defense response to bacterium / immune response / external side of plasma membrane / extracellular space / extracellular exosome / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Valjakka, J. / Hemminki, A. / Niemi, S. / Soderlund, H. / Takkinen, K. / Rouvinen, J. | ||||||
![]() | ![]() Title: Crystal Structure of an in Vitro Affinity- and Specificity-matured Anti-testosterone Fab in Complex with Testosterone. IMPROVED AFFINITY RESULTS FROM SMALL STRUCTURAL CHANGES WITHIN THE VARIABLE DOMAINS Authors: Valjakka, J. / Hemminki, A. / Niemi, S. / Soderlund, H. / Takkinen, K. / Rouvinen, J. | ||||||
History |
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Remark 999 | sequence an appropriate sequence database reference was not available at the time of processing. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.8 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.8 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Antibody | Mass: 24151.910 Da / Num. of mol.: 1 / Fragment: fab77 fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23583.697 Da / Num. of mol.: 1 / Fragment: fab77 fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.47 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: peg3350, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Details: Valjakka, J., (2002) J.Biol.Chem., 277, 4183. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 23, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→99 Å / Num. obs: 22855 / % possible obs: 93.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 87.9 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 500 Å / Num. obs: 25386 / Num. measured all: 120393 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 87.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 500 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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