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Yorodumi- PDB-5wqw: X-ray structure of catalytic domain of autolysin from Clostridium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wqw | |||||||||
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Title | X-ray structure of catalytic domain of autolysin from Clostridium perfringens | |||||||||
Components | N-acetylglucosaminidase | |||||||||
Keywords | HYDROLASE / autolysin / glycoside hydrolase 73 family | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium perfringens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.76 Å | |||||||||
Authors | Tamai, E. / Sekiya, H. / Goda, E. / Makihata, N. / Maki, J. / Yoshida, H. / Kamitori, S. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: FEBS Lett. / Year: 2017 Title: Structural and biochemical characterization of the Clostridium perfringens autolysin catalytic domain Authors: Tamai, E. / Sekiya, H. / Goda, E. / Makihata, N. / Maki, J. / Yoshida, H. / Kamitori, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wqw.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wqw.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wqw_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 5wqw_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 5wqw_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5wqw_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/5wqw ftp://data.pdbj.org/pub/pdb/validation_reports/wq/5wqw | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 30576.330 Da / Num. of mol.: 1 / Fragment: autolysin catalytic domain, UNP residues 871-1129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria) Strain: 13 / Type A / Gene: CPE1231 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XL11 | ||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
-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: 35.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1M CHES PH9.5, 10% (W/V) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→42.87 Å / Num. obs: 22481 / % possible obs: 96 % / Redundancy: 3.68 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / CC1/2: 0.852 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Resolution: 1.76→42.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.09 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.111
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.89 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→42.87 Å
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Refine LS restraints |
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