[English] 日本語
![](img/lk-miru.gif)
- PDB-1m71: Crystal structure of a Monoclonal Fab Specific for Shigella Flexn... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1m71 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a Monoclonal Fab Specific for Shigella Flexneri Y lipopolysaccharide | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / Fab-carbohydrate interactions / anti-carbohydrate antibody / X-ray Diffracrion / Shigella O-antigen | ||||||
Function / homology | ![]() immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / immune response / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A. | ||||||
![]() | ![]() Title: Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodyanamics Authors: Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A. #1: ![]() Title: Preliminary Crystallographic Analysis of a Fab Specific for the O-antigen of Shigella flexneri Cell Surface Lipopolysaccharide with and without Bound Saccharides Authors: Vyas, N.K. / Vyas, M.N. / Meikkle, P.J. / Sinnott, B. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE AT THE TIME OF PROCESSING, THIS SEQUENCE OF CHAIN A AND CHAIN B HAVE NOT YET BEEN ...SEQUENCE AT THE TIME OF PROCESSING, THIS SEQUENCE OF CHAIN A AND CHAIN B HAVE NOT YET BEEN DEPOSITED IN A SEQUENCE DATABASE. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 91.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 73.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 399.6 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m7dC ![]() 1m7iC ![]() 1mpcS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 23717.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Antibody | Mass: 23547.361 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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 45.46 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: MPD, potassium phosphate, pH 6.5, VAPOR DIFFUSION, temperature 277K |
Crystal grow | *PLUS Details: Vyas, M.N., (1993) J. Mol. Biol., 231, 133. |
-Data collection
Diffraction | Mean temperature: 281 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 2, 1990 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 10392 / % possible obs: 77.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 6 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.08 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.8→2.97 Å / Num. unique all: 1236 / % possible all: 59.9 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 108812 |
Reflection shell | *PLUS % possible obs: 59.9 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MPC Resolution: 2.8→19.76 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 38035.32 / Data cutoff high rms absF: 38035.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber Details: Author states residues 127-135 of chain B is part of a disordered segment, Bulk Solvent Model Used.
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.201803 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.76 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.292 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.41 |