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Yorodumi- PDB-4zhw: Crystal structure of a bacterial signalling protein (N-terminal t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zhw | ||||||
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Title | Crystal structure of a bacterial signalling protein (N-terminal truncation) | ||||||
Components | YfiB | ||||||
Keywords | SIGNALING PROTEIN / Outer membrane protein / signalling | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.391 Å | ||||||
Authors | Li, S. / Li, T. / Wang, Y. / Bartlam, M. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structural insights into YfiR sequestering by YfiB in Pseudomonas aeruginosa PAO1 Authors: Li, S. / Li, T. / Xu, Y. / Zhang, Q. / Zhang, W. / Che, S. / Liu, R. / Wang, Y. / Bartlam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zhw.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zhw.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/4zhw ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zhw | HTTPS FTP |
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-Related structure data
Related structure data | 4zhuC 4zhvSC 4zhyC 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: 18433.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4L6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.5M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→50 Å / Num. obs: 27019 / % possible obs: 99 % / Redundancy: 10 % / Net I/σ(I): 27.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZHV Resolution: 1.391→36.007 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.18 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.391→36.007 Å
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Refine LS restraints |
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LS refinement shell |
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