+Open data
-Basic information
Entry | Database: PDB / ID: 8oye | ||||||
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Title | Clostridium perfringens chitinase CP4_3455 E196Q with chitin | ||||||
Components | Chitodextrinase | ||||||
Keywords | HYDROLASE / chitinase / TIM / substrate / 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
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Citation | Journal: To Be Published Title: Clostridium perfringens chitinase CP4_3455 E196Q with chitin Authors: Bloch, Y. / Savvides, S.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oye.cif.gz | 427.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oye.ent.gz | 295.1 KB | Display | PDB format |
PDBx/mmJSON format | 8oye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/8oye ftp://data.pdbj.org/pub/pdb/validation_reports/oy/8oye | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 65171.520 Da / Num. of mol.: 1 / Mutation: E196Q active site mutant Source method: isolated from a genetically manipulated source Details: Residues [1-2] (MG) cloning scar / start codon. Truncated construct compared to WT. Residues [569-] (SHHHHHH) cloning scar and purification tag. Present during crystallization. Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CP4_3455 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express lysY/Iq / References: UniProt: F8UNI5 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-DMS / |
#4: 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: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop Details: PEGION A1: 0.2 M Sodium fluoride 20% w/v Polyethylene glycol 3,350, 1mM chitin hexamer (seeded) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2019 | ||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→77.95 Å / Num. obs: 134505 / % possible obs: 99.3 % / Redundancy: 12.01 % / Biso Wilson estimate: 17.66 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.058 / Net I/σ(I): 23.82 | ||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→77.95 Å / SU ML: 0.1176 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.4072 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→77.95 Å
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Refine LS restraints |
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LS refinement shell |
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