[English] 日本語
![](img/lk-miru.gif)
- PDB-1a2y: HEN EGG WHITE LYSOZYME, D18A MUTANT, IN COMPLEX WITH MOUSE MONOCL... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1a2y | ||||||
---|---|---|---|---|---|---|---|
Title | HEN EGG WHITE LYSOZYME, D18A MUTANT, IN COMPLEX WITH MOUSE MONOCLONAL ANTIBODY D1.3 | ||||||
![]() |
| ||||||
![]() | COMPLEX (IMMUNOGLOBULIN/HYDROLASE) / COMPLEX (IMMUNOGLOBULIN-HYDROLASE) / IMMUNOGLOBULIN V REGION / ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tsuchiya, D. / Mariuzza, R.A. | ||||||
![]() | ![]() Title: A mutational analysis of binding interactions in an antigen-antibody protein-protein complex. Authors: Dall'Acqua, W. / Goldman, E.R. / Lin, W. / Teng, C. / Tsuchiya, D. / Li, H. / Ysern, X. / Braden, B.C. / Li, Y. / Smith-Gill, S.J. / Mariuzza, R.A. #1: ![]() Title: Hydrogen Bonding and Solvent Structure in an Antigen-Antibody Interface. Crystal Structures and Thermodynamic Characterization of Three Fv Mutants Complexed with Lysozyme Authors: Fields, B.A. / Goldbaum, F.A. / Dall'Acqua, W. / Malchiodi, E.L. / Cauerhff, A. / Schwarz, F.P. / Ysern, X. / Poljak, R.J. / Mariuzza, R.A. #2: ![]() Title: Bound Water Molecules and Conformational Stabilization Help Mediate an Antigen-Antibody Association Authors: Bhat, T.N. / Bentley, G.A. / Boulot, G. / Greene, M.I. / Tello, D. / Dall'Acqua, W. / Souchon, H. / Schwarz, F.P. / Mariuzza, R.A. / Poljak, R.J. #3: ![]() Title: Solvent Rearrangement in an Antigen-Antibody Interface Introduced by Site-Directed Mutagenesis of the Antibody Combining Site Authors: Ysern, X. / Fields, B.A. / Bhat, T.N. / Goldbaum, F.A. / Dall'Acqua, W. / Schwarz, F.P. / Poljak, R.J. / Mariuzza, R.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 89.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1vfbS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 11700.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Antibody | Mass: 12857.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 14287.150 Da / Num. of mol.: 1 / Mutation: D18A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-PO4 / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.35 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | pH: 6.5 / Details: pH 6.5 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jul 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Highest resolution: 1.5 Å / Num. obs: 59595 / % possible obs: 90.4 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.301 / % possible all: 30.1 |
Reflection | *PLUS Num. measured all: 403840 |
Reflection shell | *PLUS % possible obs: 50.6 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB ENTRY 1VFB Resolution: 1.5→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 3
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.55 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|