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Yorodumi- PDB-3wp8: Acinetobacter sp. Tol 5 AtaA C-terminal Ylhead fused to GCN4 adap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wp8 | ||||||
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Title | Acinetobacter sp. Tol 5 AtaA C-terminal Ylhead fused to GCN4 adaptors (Chead) | ||||||
Components | Trimeric autotransporter adhesin | ||||||
Keywords | CELL ADHESION / adhesin / trimeric autotransporter adhesin / TAA / nanofiber / Ylhead / FGG / beta roll / HIM1 / adhesion | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Koiwai, K. / Hartmann, M.D. / Yoshimoto, S. / Nur 'Izzah, N. / Suzuki, A. / Linke, D. / Lupas, A.N. / Hori, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Basis for Toughness and Flexibility in the C-terminal Passenger Domain of an Acinetobacter Trimeric Autotransporter Adhesin. Authors: Koiwai, K. / Hartmann, M.D. / Linke, D. / Lupas, A.N. / Hori, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wp8.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wp8.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wp8_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
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Full document | 3wp8_full_validation.pdf.gz | 426.9 KB | Display | |
Data in XML | 3wp8_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3wp8_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wp8 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wp8 | HTTPS FTP |
-Related structure data
Related structure data | 3wpaC 3wpoC 3wppC 3wprC 3wqaC 3ntnS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34385.039 Da / Num. of mol.: 1 / Fragment: UNP residues 2905-3168 / Mutation: P3061G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter (bacteria) / Strain: Tol 5 / Gene: ataA / Plasmid: pIBA-GCN4tri / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: K7ZP88 |
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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: 2.62 Å3/Da / Density % sol: 53.02 % / Mosaicity: 0.954 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: 3% PEG 6000, 1.0M NaCl, 0.1M Na-acetate, pH 3.6, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Fixed exit Si (111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.97→50 Å / Num. all: 24269 / Num. obs: 24269 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.069 / Χ2: 2.337 / Net I/σ(I): 14.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NTN Resolution: 1.97→19.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.836 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 98.23 Å2 / Biso mean: 41.2606 Å2 / Biso min: 14.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→19.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.973→2.024 Å / Total num. of bins used: 20
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