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Yorodumi- PDB-3wpa: Acinetobacter sp. Tol 5 AtaA C-terminal stalk_FL fused to GCN4 ad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wpa | ||||||
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Title | Acinetobacter sp. Tol 5 AtaA C-terminal stalk_FL fused to GCN4 adaptors (CstalkFL) | ||||||
Components | Trimeric autotransporter adhesin | ||||||
Keywords | CELL ADHESION / adhesin / trimeric autotransporter adhesin / TAA / nanofiber / FGG / GANG / GIN / YDD / DALL3 / adhesion | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 | 3wpa.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wpa.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wpa_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
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Full document | 3wpa_full_validation.pdf.gz | 433.6 KB | Display | |
Data in XML | 3wpa_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3wpa_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wpa ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wpa | HTTPS FTP |
-Related structure data
Related structure data | 3wp8C 3wpoSC 3wppC 3wprC 3wqaC 2ynyS 3d9xS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44027.836 Da / Num. of mol.: 1 / Fragment: UNP residues 3170-3561 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: Chemical | ChemComp-CL / |
#3: 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: 2.9 Å3/Da / Density % sol: 57.57 % / Mosaicity: 0.675 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 1.26M NaH2PO4, 0.14M K2HPO4, pH 5.1, 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: 1.79→50 Å / Num. all: 50426 / Num. obs: 50426 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.112 / Χ2: 3.198 / Net I/σ(I): 8.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3d9x, 2yny, 3WPO Resolution: 1.79→33.16 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.089 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102 / 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: 147.36 Å2 / Biso mean: 42.385 Å2 / Biso min: 12.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→33.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.789→1.835 Å / Total num. of bins used: 20
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