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Yorodumi- PDB-7d6p: X-ray structure of the intermolecular complex of Clostridium perf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d6p | ||||||
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Title | X-ray structure of the intermolecular complex of Clostridium perfringens sortase C with the C-terminal cell wall sorting signal motif. | ||||||
Components | Sortase family protein | ||||||
Keywords | TRANSFERASE / cysteine transpeptidase / complex | ||||||
Function / homology | Sortase C / Sortase family / Sortase domain superfamily / Sortase domain / hydrolase activity / membrane / Sortase family protein Function and homology information | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Kamitori, S. / Tamai, E. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d6p.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d6p.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 7d6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d6p_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 7d6p_full_validation.pdf.gz | 457.1 KB | Display | |
Data in XML | 7d6p_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7d6p_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/7d6p ftp://data.pdbj.org/pub/pdb/validation_reports/d6/7d6p | HTTPS FTP |
-Related structure data
Related structure data | 7d6tC 6ixzS S: Starting model for refinement C: citing same article (ref.) |
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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: 24830.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (strain SM101 / Type A) (bacteria) Gene: CPR_0146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SWL7 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (w/v) PEG 3350, 200mM LiSO4, 100mM Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 26, 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: 2.38→18.8 Å / Num. obs: 11342 / % possible obs: 98.6 % / Redundancy: 10.5 % / CC1/2: 0.997 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.38→2.44 Å / Num. unique obs: 825 / CC1/2: 0.909 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IXZ Resolution: 2.38→18.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.162 / SU ML: 0.252 / Cross valid method: FREE R-VALUE / ESU R: 0.353 / ESU R Free: 0.257 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: 74.757 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→18.8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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