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- PDB-8gsy: X-ray structure of Clostridium perfringens pili protein B N-termi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gsy | ||||||
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Title | X-ray structure of Clostridium perfringens pili protein B N-terminal domain | ||||||
![]() | Peptidoglycan bound protein | ||||||
![]() | PROTEIN FIBRIL / Pili protein | ||||||
Function / homology | Collagen binding domain / Collagen binding domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / collagen binding / cell adhesion / extracellular region / membrane / Peptidoglycan bound protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kamitori, S. / Yamada, M. / Tamai, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biochemical characterization of Clostridium perfringens pili protein B collagen-binding domains. Authors: Tamai, E. / Yamada, M. / Ishida, T. / Arimura, N. / Matsunami, R. / Sekiya, H. / 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 | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | 88 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.5 KB | Display | ![]() |
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Full document | ![]() | 432 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gsxSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 16368.459 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 50 mM bis-tris pH 6.5, 50 mM ammonium sulfate, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→48.48 Å / Num. obs: 39168 / % possible obs: 99.98 % / Redundancy: 9.4 % / CC1/2: 0.999 / Net I/σ(I): 23.23 |
Reflection shell | Resolution: 1.55→1.59 Å / Num. unique obs: 2809 / CC1/2: 0.789 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8GSX Resolution: 1.55→48.48 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.51 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.09 / 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: 31.172 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→48.48 Å
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Refine LS restraints |
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