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- PDB-1jgl: Crystal structure of immunoglobulin Fab fragment complexed with 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jgl | ||||||
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Title | Crystal structure of immunoglobulin Fab fragment complexed with 17-beta-estradiol | ||||||
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![]() | IMMUNE SYSTEM / antibody / four-center hydrogen bond / steroid | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lamminmaki, U. / Kankare, J.A. | ||||||
![]() | ![]() Title: Crystal structure of a recombinant anti-estradiol Fab fragment in complex with 17beta -estradiol. Authors: Lamminmaki, U. / Kankare, J.A. #1: ![]() Title: Crystallization and preliminary X-ray analysis of a recombinant Fab fragment in complex with 17-beta-estradiol Authors: Lamminmaki, U. / Kankare, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.7 KB | Display | ![]() |
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PDB format | ![]() | 77.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 711.4 KB | Display | ![]() |
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Full document | ![]() | 715.7 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jhkC ![]() 1fdlS ![]() 1tetS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23665.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23460.309 Da / Num. of mol.: 1 / Fragment: residues 1-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-EST / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.1 Details: PEG4000, PEG8000, Tris-HCl, pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
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: 2.15→50 Å / Num. all: 25614 / Num. obs: 25614 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.135 / % possible all: 71.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Combination PDB entries 1TET (heavy chain variable domain)and 1FDL (light chain variable domain and both constant_1 domains) Resolution: 2.15→46.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 450405.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.54 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→46.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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