+Open data
-Basic information
Entry | Database: PDB / ID: 6ixz | ||||||
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Title | X-ray structure of sortase C from Clostridium perfringens SM101 | ||||||
Components | Sortase family protein | ||||||
Keywords | TRANSFERASE / sortase / cysteine transpeptidase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Kamitori, S. / Tamai, E. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Structures of major pilins in Clostridium perfringens demonstrate dynamic conformational change. Authors: Tamai, E. / Katayama, S. / Sekiya, H. / Nariya, 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 | 6ixz.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ixz.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ixz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/6ixz ftp://data.pdbj.org/pub/pdb/validation_reports/ix/6ixz | HTTPS FTP |
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-Related structure data
Related structure data | 5xcbC 5xccC 6ixyC 4d7wS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25036.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (strain SM101 / Type A) (bacteria) Strain: SM101 / Type A / Gene: CPR_0146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SWL7 #2: 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: 1.98 Å3/Da / Density % sol: 37.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM MMT buffer pH 6.5 (20mM L-malic acid, 40mM MES, 40mM Tris), 25% w/v PEG 1500 |
-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 / Detector: IMAGE PLATE / Date: Oct 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→19.63 Å / Num. obs: 27084 / % possible obs: 98.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.98→2.03 Å / Rmerge(I) obs: 0.336 / Num. unique obs: 1996 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D7W Resolution: 1.98→19.63 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.455 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.196 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.154 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→19.63 Å
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Refine LS restraints |
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