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Yorodumi- PDB-8c6z: necrotic enteritis associated Clostridium p. chitinase F8UNI4 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c6z | ||||||
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Title | necrotic enteritis associated Clostridium p. chitinase F8UNI4 in complex with inhibitor bisdionin C | ||||||
Components | Chitinase B | ||||||
Keywords | HYDROLASE / GH18 / enzyme / inhibitor / chitinase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Bloch, Y. / Savvides, S.N. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: Contribution and structural characterization of Chitinases to Clostridium perfringens Pathogenesis in Broilers Authors: Bloch, Y. / Dierick, E. / Goossens, E. / 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 | 8c6z.cif.gz | 249.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c6z.ent.gz | 198.3 KB | Display | PDB format |
PDBx/mmJSON format | 8c6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c6z_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8c6z_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8c6z_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 8c6z_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/8c6z ftp://data.pdbj.org/pub/pdb/validation_reports/c6/8c6z | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 69484.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 600 onwards stem from the vector. Residues [608-621] V5 epitope tag. Residues [625-630] 6His tag. Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CP4_3454, pNetB_00069 / Plasmid: pBAD TOPO TA / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: F8UNI4 | ||||||
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#2: Chemical | ChemComp-CO / | ||||||
#3: Chemical | #4: Chemical | #5: 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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop Details: 5mM CoCl2,5mM NiCl2,5 mM CdCl2, 5mM MgCl2,100mM HEPES pH7.5, 12% PEG 3350. Cryoprotected with 20% ethylene glycol prior to vitrification. |
-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: 0.97625 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→58.6 Å / Num. obs: 70266 / % possible obs: 98 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.48 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.1 / Net I/σ(I): 12.61 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: F8UNI5 Resolution: 1.85→48.94 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.77 / Stereochemistry target values: ML
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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 max: 87.77 Å2 / Biso mean: 39.8644 Å2 / Biso min: 22.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→48.94 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain A |