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- PDB-1d6v: CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-CO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d6v | ||||||
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Title | CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION | ||||||
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![]() | IMMUNE SYSTEM | ||||||
Function / homology | ![]() IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / immunoglobulin complex / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / immunoglobulin complex / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mundorff, E.C. / Hanson, M.A. / Schultz, P.G. / Stevens, R.C. | ||||||
![]() | ![]() Title: Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement. Authors: Mundorff, E.C. / Hanson, M.A. / Varvak, A. / Ulrich, H. / Schultz, P.G. / Stevens, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.6 KB | Display | ![]() |
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PDB format | ![]() | 77.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.6 KB | Display | ![]() |
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Full document | ![]() | 466.9 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 19.2 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: 23506.186 Da / Num. of mol.: 1 Fragment: chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104) Source method: isolated from a genetically manipulated source Details: THE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. THE VARIABLE DOMAINS (CHAINS A,L 1-107, CHAINS B,H 1-113) ARE MURINE. THE CONSTANT DOMAINS (CHAINS A, L 108-211 AND CHAINS B,H 113-214) ARE HUMAN. Source: (gene. exp.) ![]() ![]() ![]() Genus: Mus, Homo / Species: , / Gene: IGKC / Production host: ![]() ![]() | ||||
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#2: Antibody | Mass: 23618.234 Da / Num. of mol.: 1 Fragment: chimeric fab fragment (UNP K7T9I5 residues 1-112, P0DOX5 residues 120-220) Source method: isolated from a genetically manipulated source Details: THE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. THE VARIABLE DOMAINS (CHAINS A,L 1-107, CHAINS B,H 1-113) ARE MURINE. THE CONSTANT DOMAINS (CHAINS A, L 108-211 AND CHAINS B,H 113-214) ARE HUMAN. Source: (gene. exp.) ![]() ![]() ![]() Genus: Mus, Homo / Species: , / Production host: ![]() ![]() References: UniProt: K7T9I5, UniProt: P0DOX5, UniProt: P01857*PLUS | ||||
#3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-HOP / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 9% polyethylene glycol 4000 250mM ammonium sulfate 80mM Cadmium Chloride 75mM Hepes 20% 1,4 butanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 19K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. all: 78215 / Num. obs: 66483 / % possible obs: 85.2 % / Observed criterion σ(I): 12 / Redundancy: 2.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12 |
Reflection | *PLUS Num. obs: 28062 / Num. measured all: 66483 |
Reflection shell | *PLUS % possible obs: 83 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 7 |
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Processing
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Refinement | Resolution: 2→9.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1265132.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.28 Å2 / ksol: 0.459 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→9.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.265 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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