[English] 日本語
![](img/lk-miru.gif)
- PDB-2enr: CO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH CADMIUM HAVING A ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2enr | ||||||
---|---|---|---|---|---|---|---|
Title | CO-CRYSTALS OF DEMETALLIZED CONCANAVALIN A WITH CADMIUM HAVING A CADMIUM ION BOUND IN BOTH THE S1 SITE AND THE S2 SITE | ||||||
![]() | CONCANAVALIN A | ||||||
![]() | LECTIN / CONCANAVALIN A / PLANT LECTIN / CARBOHYDRATE BINDING / METAL BINDING / CADMIUM | ||||||
Function / homology | ![]() regulation of defense response to virus / D-mannose binding / defense response / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bouckaert, J. / Loris, R. / Wyns, L. | ||||||
![]() | ![]() Title: Zinc/calcium- and cadmium/cadmium-substituted concanavalin A: interplay of metal binding, pH and molecular packing. Authors: Bouckaert, J. / Loris, R. / Wyns, L. #1: ![]() Title: Changes in Crystal Space Group and Multimeric Structure of Concanavalin a as a Function of Metal Ion Binding and Ph Authors: Bouckaert, J. / Loris, R. / Wyns, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 54.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 418.4 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3enrC ![]() 1conS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | THE ASYMMETRIC UNIT CONTAINS A MONOMER OF 237 AMINO ACIDS. THE BIOLOGICALLY ACTIVE UNIT IS A CANONICAL DIMER (BELOW PH 6) OR TETRAMER. THE FOLLOWING SURFACE LOOPS ARE IN WEAK ELECTRON DENSITY: 118-123 AND 160-163. A CD2+ IS SUBSTITUTED FOR MN2+ IN THE TRANSITION METAL ION SITE S1. A CD2+ IS SUBSTITUTED FOR CA2+ IN THE CALCIUM SITE S2. |
-
Components
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CADMIUM/CADMIUM COMPLEX / Source: (natural) ![]() ![]() | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 39.8 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5 / Details: pH 5.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 291 K |
---|---|
Diffraction source | Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 13, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→11 Å / Num. obs: 30650 / % possible obs: 96.02 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.38→2.45 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.299 / % possible all: 80.9 |
Reflection | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 10 Å / Num. obs: 10111 / % possible obs: 95.3 % / Num. measured all: 30650 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 2.35 Å / Lowest resolution: 2.46 Å / % possible obs: 75.1 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 10.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CON Resolution: 2.35→10 Å / Isotropic thermal model: RESTRAINED / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.42 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.262 |