[English] 日本語
![](img/lk-miru.gif)
- PDB-1dyp: 1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1dyp | ||||||
---|---|---|---|---|---|---|---|
Title | 1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE | ||||||
![]() | KAPPA-CARRAGEENASE | ||||||
![]() | HYDROLASE / KAPPA-CARRAGEENAN DOUBLE HELIX DEGRADATION | ||||||
Function / homology | ![]() kappa-carrageenase / kappa-carrageenase activity / periplasmic space / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Michel, G. / Chantalat, L. / Dideberg, O. | ||||||
![]() | ![]() Title: The Kappa-Carrageenase of P. Carrageenovora Features a Tunnel-Shaped Active Site: A Novel Insight in the Evolution of Clan-B Glycoside Hydrolases Authors: Michel, G. / Chantalat, L. / Duee, E. / Barbeyron, T. / Henrissat, B. / Kloareg, B. / Dideberg, O. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Expression, Purification, Crystallization and Preliminary X-Ray Analysis of the Kappa-Carrageenase from Pseudoalteromonas Carrageenovora. Authors: Michel, G. / Barbeyron, T. / Flament, D. / Vernet, T. / Kloareg, B. / Dideberg, O. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 76 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31559.338 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH CADMIUM CHLORIDE Source: (gene. exp.) ![]() Description: PROCESSED PROTEIN, HIS-TAG, SELEMETHIONYL PROTEIN Gene: CGKA / Plasmid: PET20B / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.019 Å3/Da / Density % sol: 40.38 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.5 / Details: pH 4.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 285 K / pH: 7.2 / Method: vapor diffusion, hanging dropDetails: Michel, G., (1999) Acta Crystallogr.,Sect.D, D55, 918. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 16, 1999 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.54→24.25 Å / Num. obs: 38205 / % possible obs: 97.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 12.5 Å2 / Rsym value: 0.03 / Net I/σ(I): 16.1 | ||||||||||||
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 6.2 / Rsym value: 0.116 / % possible all: 81.3 | ||||||||||||
Reflection | *PLUS Redundancy: 3.15 % / Num. measured all: 120447 / Rmerge(I) obs: 0.03 | ||||||||||||
Reflection shell | *PLUS % possible obs: 81.3 % / Rmerge(I) obs: 0.116 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: THE FOLLOWING RESIDUES HAVE TWO CONFORMATIONS, MET 28, SER 199, LYS 277, SER 285, GLU 287.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.427 Å2 / ksol: 0.33629 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→24.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.54→1.64 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|