[English] 日本語
Yorodumi- PDB-9ijc: Crystal structure of the beta,kappa-carrageenase Cgbk16A from Wen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ijc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the beta,kappa-carrageenase Cgbk16A from Wenyingzhuangia fucanilytica | ||||||
Components | GH16 domain-containing protein | ||||||
Keywords | HYDROLASE / Apo / Carrageenase / GH16_13 / Glucoside hydrolase | ||||||
Function / homology | Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / GH16 domain-containing protein Function and homology information | ||||||
Biological species | Wenyingzhuangia fucanilytica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Chang, Y. / Chen, F. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: Structural insights into the substrate recognition and catalytic mechanism of a beta,kappa-carrageenase from Wenyingzhuangia fucanilytica Authors: Chang, Y. / Chen, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9ijc.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9ijc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9ijc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ijc_validation.pdf.gz | 352.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9ijc_full_validation.pdf.gz | 354.5 KB | Display | |
Data in XML | 9ijc_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 9ijc_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/9ijc ftp://data.pdbj.org/pub/pdb/validation_reports/ij/9ijc | HTTPS FTP |
-Related structure data
Related structure data | 9intC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37279.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria) Gene: AXE80_10150 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B1Y771 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.69 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 25.5% PEG 4000, 15% Glycerol, 0.17 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50.16 Å / Num. obs: 55782 / % possible obs: 97.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05349 / Rpim(I) all: 0.01554 / Rrim(I) all: 0.05577 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.2553 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5175 / CC1/2: 0.986 / Rpim(I) all: 0.07313 / Rrim(I) all: 0.2658 / % possible all: 94.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→50.16 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.49 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→50.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|