[English] 日本語
Yorodumi- PDB-8ose: C. perfringens chitinase CP4_3455 in complex with inhibitor bisdi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ose | ||||||
---|---|---|---|---|---|---|---|
Title | C. perfringens chitinase CP4_3455 in complex with inhibitor bisdionin C | ||||||
Components | Chitodextrinase | ||||||
Keywords | HYDROLASE / chitinase / inhibitor / TIM barrel / necrotic enteritis | ||||||
Function / homology | Function and homology information polysaccharide binding / chitin binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Bloch, Y. / Savvides, S.N. | ||||||
Funding support | Belgium, 1items
| ||||||
Citation | Journal: To Be Published Title: C. perfringens chitinase CP4_3455 in complex with inhibitor bisdionin C Authors: Bloch, Y. / Savvides, S.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ose.cif.gz | 384.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ose.ent.gz | 288.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ose.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/8ose ftp://data.pdbj.org/pub/pdb/validation_reports/os/8ose | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 65172.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues [1-2 (MG)] cloning scar. Residues [569-575 (SHHHHHH)] purification tag. Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CP4_3455 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq / References: UniProt: F8UNI5 |
---|---|
#2: Chemical | ChemComp-DW0 / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % |
---|---|
Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 0.2 M Lithium acetate dihydrate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.35→49.47 Å / Num. obs: 133165 / % possible obs: 99.1 % / Redundancy: 5.78 % / Biso Wilson estimate: 17.24 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.044 / Net I/σ(I): 18.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→49.47 Å / SU ML: 0.1055 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.1431 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→49.47 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 11.342 Å / Origin y: 1.746 Å / Origin z: 5.512 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ( CHAIN A AND RESID 701:701 ) |