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Open data
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Basic information
Entry | Database: PDB / ID: 1jv5 | ||||||
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Title | Anti-blood group A Fv | ||||||
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![]() | Immune System / Sugar Binding Protein / immunoglobulin | ||||||
Function / homology | ![]() CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thomas, R. / Patenaude, S.I. / MacKenzie, C.R. / To, R. / Hirama, T. / Young, N.M. / Evans, S.V. | ||||||
![]() | ![]() Title: Structure of an anti-blood group A Fv and improvement of its binding affinity without loss of specificity. Authors: Thomas, R. / Patenaude, S.I. / MacKenzie, C.R. / To, R. / Hirama, T. / Young, N.M. / Evans, S.V. #1: ![]() Title: Production, crystallization and diffraction to atomic resolution of an antibody Fv specific for the blood-group A oligosaccharide antigen Authors: Patenaude, S.I. / MacKenzie, C.R. / Bilous, D. / To, R.J. / Ryan, S.E. / Young, N.M. / Evans, S.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53 KB | Display | ![]() |
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PDB format | ![]() | 41.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
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Full document | ![]() | 446.4 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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: 11809.013 Da / Num. of mol.: 1 / Fragment: anti-blood group A Fv Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 12877.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.5 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, HEPES, Calcium Chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Patenaude, S.I., (1998) Acta Crystallogr., Sect.D, 54, 1456.pH: 8 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 15, 1994 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 12350 / Num. obs: 12350 / % possible obs: 93 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 2.2→2.31 Å / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 9.3 / Num. unique all: 674 / % possible all: 71.8 |
Reflection | *PLUS Num. obs: 12348 / Num. measured all: 24752 / Rmerge(I) obs: 0.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→3.21 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection all: 12348 / σ(F): 3 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.256 / Rfactor Rwork: 0.203 |