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Yorodumi- PDB-9int: Crystal structure of the complex of the beta,kappa-carrageenase C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9int | ||||||
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Title | Crystal structure of the complex of the beta,kappa-carrageenase Cgbk16A from Wenyingzhuangia fucanilytica with an oligosaccharide of furcellaran | ||||||
Components | GH16 domain-containing protein | ||||||
Keywords | HYDROLASE / complex / Carrageenase / GH16_13 / Glucoside hydrolase / oligotetrasaccharide / furcellaran | ||||||
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: 1.56 Å | ||||||
Authors | Chang, Y. / Chen, F. | ||||||
Funding support | 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9int.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9int.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9int.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9int_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 9int_full_validation.pdf.gz | 473 KB | Display | |
Data in XML | 9int_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 9int_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/9int ftp://data.pdbj.org/pub/pdb/validation_reports/in/9int | HTTPS FTP |
-Related structure data
Related structure data | 9ijcC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 |
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#2: Polysaccharide | 3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha- ...3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose Type: oligosaccharide / Mass: 1096.941 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.94 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 25.5% PEG 4000, 15% Glycerol, 0.17 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 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: 1.56→40.58 Å / Num. obs: 52972 / % possible obs: 97.86 % / Redundancy: 12.7 % / Biso Wilson estimate: 20.59 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 1.56→1.62 Å / Mean I/σ(I) obs: 5.5 / Num. unique obs: 51770 / CC1/2: 0.963 / % possible all: 93.74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→40.58 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 17.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→40.58 Å
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Refine LS restraints |
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LS refinement shell |
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