+Open data
-Basic information
Entry | Database: PDB / ID: 1ub6 | ||||||
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Title | Crystal structure of Antibody 19G2 with sera ligand | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody fluorscence dynamics / sera ligand | ||||||
Function / homology | Function and homology information 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 / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Beuscher, A.B. / Wirsching, P. / Lerner, R.A. / Janda, K. / Stevens, R.C. | ||||||
Citation | Journal: To be published Title: Structure and Dynamics of Blue Fluorescent Antibody 19G2 at Blue and Violet Fluorescent Temperatures Authors: Beuscher, A.B. / Wirsching, P. / Lerner, R.A. / Janda, K. / Stevens, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ub6.cif.gz | 176.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ub6.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ub6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/1ub6 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/1ub6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21943.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell / Production host: Mus musculus (house mouse) / References: UniProt: P18527, UniProt: P01867*PLUS #2: Protein | Mass: 23209.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell / Production host: Mus musculus (house mouse) / References: UniProt: P01837*PLUS #3: 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: 2.54 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→19.43 Å / Num. all: 50364 / Observed criterion σ(F): 0 / Biso Wilson estimate: 23.8 Å2 / Limit h max: 81 / Limit h min: -91 / Limit k max: 28 / Limit k min: -91 / Limit l max: 43 / Limit l min: 0 / Observed criterion F max: 613443.39 / Observed criterion F min: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→19.43 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 64.5179 Å2 / ksol: 0.361169 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.96 Å2 / Biso mean: 47.56 Å2 / Biso min: 1.85 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.12→19.43 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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