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Yorodumi- PDB-5xcb: X-ray structure of domains D1 and D2 of Clostridium perfringens p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xcb | ||||||
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Title | X-ray structure of domains D1 and D2 of Clostridium perfringens pili protein CppA | ||||||
Components | Probable surface protein | ||||||
Keywords | STRUCTURAL PROTEIN / pili 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 / Immunoglobulin-like fold / membrane / Probable surface protein Function and homology information | ||||||
Biological species | Clostridium perfringens str. 13 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 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 | 5xcb.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xcb.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 5xcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xcb_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
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Full document | 5xcb_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 5xcb_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 5xcb_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/5xcb ftp://data.pdbj.org/pub/pdb/validation_reports/xc/5xcb | HTTPS FTP |
-Related 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: 36464.484 Da / Num. of mol.: 1 / Fragment: UNP residues 30-337 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens str. 13 (bacteria) Strain: 13 / Gene: CPE0156 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XP10 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.06M Magnesium chloride hexahydrate, 0.06M Calcium chloride dihydrate, 0.1M Tris (base), 0.1M BICINE, 20% v/v PEG 500* MME, 10 % w/v PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→18.76 Å / Num. obs: 22094 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 22.86 |
Reflection shell | Resolution: 2.14→2.2 Å / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.01 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→18.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.681 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.19 / 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: 47.056 Å2
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Refinement step | Cycle: 1 / Resolution: 2.14→18.76 Å
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Refine LS restraints |
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