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Yorodumi- PDB-8yxk: X-ray structure of Clostridioides difficile endolysin Ecd09610 gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8yxk | ||||||
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Title | X-ray structure of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain. | ||||||
Components | Phage cell wall hydrolase | ||||||
Keywords | HYDROLASE / Clostridioides difficile / endolysin | ||||||
Function / homology | Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / amidase activity / Papain-like cysteine peptidase superfamily / Phage cell wall hydrolase Function and homology information | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Kamitori, S. / Tamai, E. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2024 Title: X-ray structure and mutagenesis analyses of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain. Authors: Sekiya, H. / Nonaka, Y. / Kamitori, S. / Miyaji, T. / Tamai, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yxk.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yxk.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 8yxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/8yxk ftp://data.pdbj.org/pub/pdb/validation_reports/yx/8yxk | HTTPS FTP |
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-Related structure data
Related structure data | 8yxnC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22397.062 Da / Num. of mol.: 2 / Fragment: glucosaminidase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (strain 630) (bacteria) Gene: CD630_09610, CD630_29030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q183Y3 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 20% (w/v) PEG 3350, 200mM sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→19.322 Å / Num. obs: 29563 / % possible obs: 98.5 % / Redundancy: 3.7 % / CC1/2: 0.996 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.87→1.92 Å / Num. unique obs: 2151 / CC1/2: 0.761 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→19.322 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.886 / SU B: 4.573 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.171 / ESU R Free: 0.161 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.628 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→19.322 Å
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Refine LS restraints |
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LS refinement shell |
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