+Open data
-Basic information
Entry | Database: PDB / ID: 6ixy | ||||||
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Title | X-ray structure of major pilin from C. perfringens SM101 | ||||||
Components | pilin | ||||||
Keywords | STRUCTURAL PROTEIN / major pilin / fiber protein | ||||||
Function / homology | Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Fimbrial isopeptide formation D2 domain / Prealbumin-like fold domain / Prealbumin-like fold domain / membrane => GO:0016020 / Immunoglobulin-like fold / Putative surface protein Function and homology information | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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 | 6ixy.cif.gz | 345.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ixy.ent.gz | 281.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ixy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ixy_validation.pdf.gz | 468.3 KB | Display | wwPDB validaton report |
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Full document | 6ixy_full_validation.pdf.gz | 483.7 KB | Display | |
Data in XML | 6ixy_validation.xml.gz | 58 KB | Display | |
Data in CIF | 6ixy_validation.cif.gz | 79.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/6ixy ftp://data.pdbj.org/pub/pdb/validation_reports/ix/6ixy | HTTPS FTP |
-Related structure data
Related structure data | 5xcbC 5xccSC 6ixzC 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 52321.914 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (strain SM101 / Type A) (bacteria) Gene: CPR_0145 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0SWL8 #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: 3.14 Å3/Da / Density % sol: 60.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 4% v/v Tacsimate buffer pH 4.0 (73mM malonic acid, 10mM ammonium citrate tribasic, 5mM succinic acid, 12mM D,L-malic acid, 16mM sodium acetate trihydrate, 20mM sodium formate, 6.4mM ammonium ...Details: 4% v/v Tacsimate buffer pH 4.0 (73mM malonic acid, 10mM ammonium citrate tribasic, 5mM succinic acid, 12mM D,L-malic acid, 16mM sodium acetate trihydrate, 20mM sodium formate, 6.4mM ammonium tartrate dibasic), 12% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→48.71 Å / Num. obs: 69104 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.72→2.79 Å / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5092 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XCC Resolution: 2.72→48.71 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.855 / SU B: 13.343 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.766 / ESU R Free: 0.354 / 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: 45.106 Å2
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Refinement step | Cycle: 1 / Resolution: 2.72→48.71 Å
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Refine LS restraints |
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