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Open data
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Basic information
Entry | Database: PDB / ID: 1n7m | ||||||
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Title | Germline 7G12 with N-methylmesoporphyrin | ||||||
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![]() | IMMUNE SYSTEM | ||||||
Function / homology | ![]() Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / antigen binding / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yin, J. / Andryski, S.E. / Beuscher IV, A.E. / Stevens, R.C. / Schultz, P.G. | ||||||
![]() | ![]() Title: Structural evidence for substrate strain in antibody catalysis Authors: Yin, J. / Andryski, S.E. / Beuscher IV, A.E. / Stevens, R.C. / Schultz, P.G. | ||||||
History |
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Remark 999 | SEQUENCE The gene sequences are derived from a mouse hybridoma. The sequences of the protein chains ...SEQUENCE The gene sequences are derived from a mouse hybridoma. The sequences of the protein chains are not found in any sequence database. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.8 KB | Display | ![]() |
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PDB format | ![]() | 82.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.8 KB | Display | ![]() |
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Full document | ![]() | 827 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.6 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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Unit cell |
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Components
#1: Antibody | Mass: 23334.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: ![]() ![]() |
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#2: Antibody | Mass: 23067.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Production host: ![]() ![]() |
#3: Chemical | ChemComp-MMP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 22% PEG2000MME, 0.2M Ammonium Sulfate, 10mM Cd Sulfate, 1mM NMP, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.79 Å / Num. all: 44580 / Num. obs: 44580 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.8 Å2 / Limit h max: 30 / Limit h min: -30 / Limit k max: 39 / Limit k min: -30 / Limit l max: 31 / Limit l min: 0 / Observed criterion F max: 1427793.72 / Observed criterion F min: 0.32 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 17466 / % possible obs: 95.5 % / Num. measured all: 125917 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 67.9 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 4.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 47.204 Å2 / ksol: 0.333298 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.86 Å2 / Biso mean: 30.79 Å2 / Biso min: 11.76 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.79 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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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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