+Open data
-Basic information
Entry | Database: PDB / ID: 5eb0 | |||||||||
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Title | crystal form II of YfiB belonging to P41 | |||||||||
Components | YfiB | |||||||||
Keywords | MEMBRANE PROTEIN / OmpA/Pal-like outer-membrane lipoprotein | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Xu, M. / Yang, X. / Yang, X.-A. / Zhou, L. / Liu, T.-Z. / Fan, Z. / Jiang, T. | |||||||||
Funding support | China, 2items
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Citation | Journal: Protein Cell / Year: 2016 Title: Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system Authors: Xu, M. / Yang, X. / Yang, X.-A. / Zhou, L. / Liu, T.-Z. / Fan, Z. / Jiang, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eb0.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eb0.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 5eb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/5eb0 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/5eb0 | HTTPS FTP |
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-Related structure data
Related structure data | 5eazC 5eb1C 5eb2C 5eb3C 3khnS 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
#1: Protein | Mass: 14876.660 Da / Num. of mol.: 2 / Fragment: UNP residues 34-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiB, PA1119 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9I4L6 #2: Chemical | ChemComp-SO4 / | #3: 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: 2.86 Å3/Da / Density % sol: 56.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl, 30%(w/v) polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 8105 / % possible obs: 97.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.146 / Χ2: 0.929 / Net I/av σ(I): 12.5 / Net I/σ(I): 8.5 / Num. measured all: 89623 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3khn Resolution: 2.8→46.953 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.28 Å2 / Biso mean: 42.5976 Å2 / Biso min: 11.34 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→46.953 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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