[English] 日本語
![](img/lk-miru.gif)
- PDB-1t2q: The Crystal Structure of an NNA7 Fab that recognizes an N-type bl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1t2q | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / Fab / glycophorin A / blood group antigen | ||||||
Function / homology | ![]() positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding ...positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / extracellular space / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xie, K. / Song, S.C. / Spitalnik, S.L. / Wedekind, J.E. | ||||||
![]() | ![]() Title: Crystal Structure and Mutational Analysis of an Antibody that Recognizes an N-type Blood Group Antigen Authors: Xie, K. / Song, S.C. / Spitalnik, S.L. / Wedekind, J.E. #1: ![]() Title: Purification, Crystallization and X-ray Diffraction Analysis of a Recombinant Fab that Recognizes a Human Blood Group antigen Authors: Song, S.C. / Xie, K. / Czerwinski, M. / Spitalnik, S.L. / Wedekind, J.E. #2: ![]() Title: Alteration of Amino Acid Residues at the L-chain N-terminus and in Complementarity-Determining Region 3 Increases Affinity of a Recombinant F(ab) for the Human N Blood Group Antigen Authors: Song, S.C. / Czerwinski, M. / Wojczyk, B.S. / Spitalnik, S.L. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE The sequence of the protein was not deposited into any sequence database. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 48g7S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit comprises the heavy and light chains that form the Fab fragment |
-
Components
#1: Antibody | Mass: 23868.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Antibody | Mass: 23574.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG MME 5K, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 11, 2003 / Details: Osmic Confocal Blue |
Radiation | Monochromator: Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→36.7 Å / Num. obs: 43775 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.293 / % possible all: 53 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 48G7 Resolution: 1.83→36.6 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.3753 Å2 / ksol: 0.385562 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→36.6 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.83→1.94 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|