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Yorodumi- PDB-5jip: Crystal structure of the Clostridium perfringens spore cortex lyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jip | ||||||
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Title | Crystal structure of the Clostridium perfringens spore cortex lytic enzyme SleM | ||||||
Components | Cortical-lytic enzyme | ||||||
Keywords | HYDROLASE / spore / cortex / peptidoglycan-lysin | ||||||
Function / homology | Function and homology information peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chirgadze, D.Y. / Christie, G. / Ustok, F.I. / Al-Riyami, B. / Stott, K. | ||||||
Citation | Journal: Proteins / Year: 2016 Title: The crystal structure of Clostridium perfringens SleM, a muramidase involved in cortical hydrolysis during spore germination. Authors: Al-Riyami, B. / Ustok, F.I. / Stott, K. / Chirgadze, D.Y. / Christie, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jip.cif.gz | 275.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jip.ent.gz | 222.7 KB | Display | PDB format |
PDBx/mmJSON format | 5jip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jip_validation.pdf.gz | 445.1 KB | Display | wwPDB validaton report |
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Full document | 5jip_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 5jip_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 5jip_validation.cif.gz | 58.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/5jip ftp://data.pdbj.org/pub/pdb/validation_reports/ji/5jip | HTTPS FTP |
-Related structure data
Related structure data | 1jfxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37584.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: sleM / Plasmid: pBADcLIC-SleM Details (production host): arabinose inducible expression plasmid compatible with ligation independent cloning Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: O06496 #2: Chemical | ChemComp-MES / #3: Chemical | #4: 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: 2.44 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES buffer, pH 6.0, 0.25 M magnesium chloride, 16% (w/v) PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 5, 2014 / Details: HELIOS MX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.4 Å / Num. obs: 66317 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 5 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JFX Resolution: 1.8→42.397 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.397 Å
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Refine LS restraints |
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LS refinement shell |
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