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Yorodumi- PDB-5gyj: Structure of catalytically active sortase from Clostridium difficile -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gyj | ||||||
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Title | Structure of catalytically active sortase from Clostridium difficile | ||||||
Components | Putative peptidase C60B, sortase B | ||||||
Keywords | HYDROLASE / transpeptidase / Cys-His-Arg catalytic triad | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Peptoclostridium difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å | ||||||
Authors | Yin, J.-C. / Fei, C.-H. / Hsiao, Y.-Y. / Nix, J.C. / Huang, I.-H. / Wang, S. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Front Cell Infect Microbiol / Year: 2016 Title: Structural Insights into Substrate Recognition by Clostridium difficile Sortase. Authors: Yin, J.C. / Fei, C.H. / Lo, Y.C. / Hsiao, Y.Y. / Chang, J.C. / Nix, J.C. / Chang, Y.Y. / Yang, L.W. / Huang, I.H. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gyj.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gyj.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gyj_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 5gyj_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 5gyj_validation.xml.gz | 9 KB | Display | |
Data in CIF | 5gyj_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/5gyj ftp://data.pdbj.org/pub/pdb/validation_reports/gy/5gyj | HTTPS FTP |
-Related structure data
Related structure data | 1qwzS 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: 26189.283 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 28-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria) Strain: 630 / Gene: CD630_27180 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q183F3 |
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#2: 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: 2.69 Å3/Da / Density % sol: 54.29 % / Description: cubic 0.3 micrometer in diameter |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 0.1M citric acid, pH3.5, 0.1M glycine, 24% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25.9 Å / Num. obs: 7031 / % possible obs: 94.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 55.74 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 45.85 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 10.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QWZ Resolution: 2.801→25.851 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.1514 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→25.851 Å
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Refine LS restraints |
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LS refinement shell |
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