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Yorodumi- PDB-1a6v: B1-8 FV fragment complexed with a (4-hydroxy-3-nitrophenyl) aceta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a6v | |||||||||
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Title | B1-8 FV fragment complexed with a (4-hydroxy-3-nitrophenyl) acetate compound | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / HAPTEN | |||||||||
Function / homology | Function and homology information immunoglobulin complex / adaptive immune response / immune response / extracellular space Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | |||||||||
Authors | Simon, T. / Henrick, K. / Hirshberg, M. / Winter, G. | |||||||||
Citation | Journal: To be Published Title: X-Ray Structures of Fv Fragment and its (4-Hydroxy-3-Nitrophenyl)Acetate Complex of Murine B1-8 Antibody Authors: Simon, T. / Henrick, K. / Hirshberg, M. / Winter, G. #1: Journal: Protein Eng. / Year: 1992 Title: A Functional Antibody Mutant with an Insertion in the Framework Region 3 Loop of the Vh Domain: Implications for Antibody Engineering Authors: Simon, T. / Rajewsky, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a6v.cif.gz | 151.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6v.ent.gz | 121.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6v ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6v | HTTPS FTP |
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-Related structure data
Related structure data | 1a6uC 1a6wC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Antibody | Mass: 11631.869 Da / Num. of mol.: 3 / Fragment: FV FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Cell line: J558L / Organ: TAIL / Cell line (production host): J558L / Production host: Mus musculus (house mouse) / References: UniProt: P01724 #2: Antibody | Mass: 13440.945 Da / Num. of mol.: 3 / Fragment: FV FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Cell line: J558L / Organ: TAIL / Cell line (production host): J558L / Production host: Mus musculus (house mouse) / References: UniProt: P01751 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 33.2 % |
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Crystal grow | Details: CRYSTALS WERE GROWN USING AMMONIUM SULPHATE AS PRECIPITANT |
-Data collection
Diffraction | Mean temperature: 269 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→9.2 Å / Num. obs: 367775 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.361 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→6 Å / σ(F): 0 Details: THE STRUCTURE HAS THREE MOLECULES PER EQUIVALENT POSITION ARRANGED AS A TRANSLATION ALONG THE Z-AXIS SUCH THAT OVERALL THE DIFFRACTION DATA SHOWS WEAK INTENSITIES FOR HKL, L=2N AND THIS ...Details: THE STRUCTURE HAS THREE MOLECULES PER EQUIVALENT POSITION ARRANGED AS A TRANSLATION ALONG THE Z-AXIS SUCH THAT OVERALL THE DIFFRACTION DATA SHOWS WEAK INTENSITIES FOR HKL, L=2N AND THIS TRANSLATIONAL NON-CRYSTALLOGRAPHIC SYMMETRY IS ON CLEARLY BROKEN BY THE DIFFERENT CONFORMATION OF THE TAIL O HAPTEN LIGAND ADOPTED IN EACH OF THE THREE INDEPENDENTLY DETERMINED MOLECULES. THERE ARE ALSO TWO CONFORMATIONS FOUND FOR THE HAPTEN BOUND TO CHAINS L AND H.
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Displacement parameters | Biso mean: 14.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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