+Open data
-Basic information
Entry | Database: PDB / ID: 3x0u | ||||||
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Title | Crystal structure of PirB | ||||||
Components | Uncharacterized protein | ||||||
Keywords | TOXIN / seven-helix bundle / beta barrel / pore-forming toxin | ||||||
Function / homology | Pesticidal crystal protein, N-terminal domain / Delta-Endotoxin; domain 1 / Up-down Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Vibrio parahaemolyticus M0605 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Wang, H.C. / Ko, T.P. / Wang, A.H.J. / Lo, C.F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin. Authors: Lee, C.T. / Chen, I.T. / Yang, Y.T. / Ko, T.P. / Huang, Y.T. / Huang, J.Y. / Huang, M.F. / Lin, S.J. / Chen, C.Y. / Lin, S.S. / Lin, S.S. / Lightner, D.V. / Wang, H.C. / Wang, A.H. / Wang, H. ...Authors: Lee, C.T. / Chen, I.T. / Yang, Y.T. / Ko, T.P. / Huang, Y.T. / Huang, J.Y. / Huang, M.F. / Lin, S.J. / Chen, C.Y. / Lin, S.S. / Lin, S.S. / Lightner, D.V. / Wang, H.C. / Wang, A.H. / Wang, H.C. / Hor, L.I. / Lo, C.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x0u.cif.gz | 202.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x0u.ent.gz | 160.4 KB | Display | PDB format |
PDBx/mmJSON format | 3x0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x0u_validation.pdf.gz | 445.9 KB | Display | wwPDB validaton report |
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Full document | 3x0u_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | 3x0u_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 3x0u_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/3x0u ftp://data.pdbj.org/pub/pdb/validation_reports/x0/3x0u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 51257.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus M0605 (bacteria) Gene: AJ90_20625, pirB / Production host: Escherichia coli (E. coli) / References: UniProt: X7RH70 #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: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 20mM Tris, 300mM NaCl, 20% 1,4-butanediol, 0.1M Na-acetate, 15% 2,3-butanediol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 99968 / Num. obs: 99668 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→26.25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.915 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / 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: 18.691 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→26.25 Å
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Refine LS restraints |
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