[English] 日本語
![](img/lk-miru.gif)
- PDB-3jr6: Sequential reorganization of beta-sheet topology by insertion of ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3jr6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Sequential reorganization of beta-sheet topology by insertion of a single strand | |||||||||
![]() | Lysozyme | |||||||||
![]() | HYDROLASE / sequence duplication / protein design / tandem repeat / beta-sheet / Antimicrobial / Bacteriolytic enzyme / Glycosidase | |||||||||
Function / homology | ![]() viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Sagermann, M. / Baas, W.A. / Matthews, B.W. | |||||||||
![]() | ![]() Title: Sequential reorganization of beta-sheet topology by insertion of a single strand. Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W. #1: ![]() Title: Long-distance conformational changes in a protein engineered by modulated sequence duplication. Authors: Sagermann, M. / Gay, L. / Matthews, B.W. #2: ![]() Title: Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding. Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 128.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 101.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 514.9 KB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 19220.088 Da / Num. of mol.: 4 Mutation: C54T, C97A, insertion of seuqence (gighll) after residue L33 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.29 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3400, 50 mM ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 5, 1998 / Details: yale mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→32.44 Å / Num. obs: 17925 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.07 |
Reflection shell | Highest resolution: 3 Å / Rsym value: 0.097 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: T4 lysozyme I3P mutant Resolution: 3→32.44 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Authors state that scaling and B-value refinement were performed with CNS using a recommended resolution range of 6.0-3.0 A resolution. As the B-values for the data set were determined to be ...Details: Authors state that scaling and B-value refinement were performed with CNS using a recommended resolution range of 6.0-3.0 A resolution. As the B-values for the data set were determined to be low (even for higher low-resolution cut-offs), the B-values for the atoms remained similarly low as well. Molecules A and B exhibit well-defined density of the loops. The corresponding loops of molecules B and C were in poor density but could clearly be identified. Loops and terminal residues that could not be refined reliably were omitted: B(L170), D(L170), B(34-46), C(36-46).
| |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→32.44 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|