+Open data
-Basic information
Entry | Database: PDB / ID: 1i3g | ||||||
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Title | CRYSTAL STRUCTURE OF AN AMPICILLIN SINGLE CHAIN FV, FORM 1, FREE | ||||||
Components | (ANTIBODY FV FRAGMENT) x 2 | ||||||
Keywords | ANTIBIOTIC / ANTIBODY FV FRAGMENT | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Jung, S. / Spinelli, S. / Schimmele, B. / Honegger, A. / Pugliese, L. / Cambillau, C. / Pluckthun, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Selection, characterization and x-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries. Authors: Burmester, J. / Spinelli, S. / Pugliese, L. / Krebber, A. / Honegger, A. / Jung, S. / Schimmele, B. / Cambillau, C. / Pluckthun, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i3g.cif.gz | 57.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i3g.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1i3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i3g_validation.pdf.gz | 389.6 KB | Display | wwPDB validaton report |
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Full document | 1i3g_full_validation.pdf.gz | 391.3 KB | Display | |
Data in XML | 1i3g_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1i3g_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/1i3g ftp://data.pdbj.org/pub/pdb/validation_reports/i3/1i3g | HTTPS FTP |
-Related 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: 12295.677 Da / Num. of mol.: 1 / Fragment: VL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 13480.933 Da / Num. of mol.: 1 / Fragment: VH DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-MPD / ( |
#4: 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: 2.57 Å3/Da / Density % sol: 52.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium Sulfate,potassium phosphate, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / 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: 2.44→20 Å / Num. all: 41050 / Num. obs: 9809 / % possible obs: 89.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.07 / Net I/σ(I): 11 |
Reflection | *PLUS Num. measured all: 41050 |
Reflection shell | *PLUS % possible obs: 71.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: anti-N9-neuraminidase antibody NC41/anti-lysozyme antibody D11.15 Resolution: 2.44→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.44→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.175 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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