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- PDB-7d6t: X-ray structure of Clostridium perfringens sortase C with the C-t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d6t | ||||||
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Title | X-ray structure of Clostridium perfringens sortase C with the C-terminal cell wall sorting motif. | ||||||
![]() | Sortase family protein | ||||||
![]() | TRANSFERASE / cysteine transpeptidase | ||||||
Function / homology | Sortase C / Sortase family / Sortase domain superfamily / Sortase domain / hydrolase activity / membrane / Sortase family protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kamitori, S. / Tamai, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray structures of Clostridium perfringens sortase C with C-terminal cell wall sorting motif of LPST demonstrate role of subsite for substrate-binding and structural variations of catalytic site. Authors: Tamai, E. / Sekiya, H. / Nariya, H. / Katayama, S. / Kamitori, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.8 KB | Display | ![]() |
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PDB format | ![]() | 129.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436 KB | Display | ![]() |
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Full document | ![]() | 439.1 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d6pC ![]() 6ixzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24830.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CPR_0146 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 30% (w/v) PEG 4000, 200mM LiSO4, 100mM Tris-HCl, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→19.02 Å / Num. obs: 43526 / % possible obs: 97.6 % / Redundancy: 2.4 % / CC1/2: 0.998 / Net I/σ(I): 12.56 |
Reflection shell | Resolution: 1.68→1.72 Å / Num. unique obs: 3217 / CC1/2: 0.839 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6IXZ Resolution: 1.68→19.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.697 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.313 Å2
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Refinement step | Cycle: 1 / Resolution: 1.68→19.02 Å
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Refine LS restraints |
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