+Open data
-Basic information
Entry | Database: PDB / ID: 5eb3 | |||||||||
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Title | VB6-bound protein | |||||||||
Components | YfiR | |||||||||
Keywords | TRANSCRIPTION / PERIPLASMIC REPRESSOR PROTEIN | |||||||||
Function / homology | YfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol / Negative regulator YfiR Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 5eb3.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eb3.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 5eb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/5eb3 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/5eb3 | HTTPS FTP |
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-Related structure data
Related structure data | 5eazC 5eb0C 5eb1C 5eb2C 4yn7S 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: 17392.783 Da / Num. of mol.: 2 / Fragment: UNP residues 35-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiR, PA1121 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9I4L4 #2: Chemical | #3: Chemical | ChemComp-UEG / | #4: 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: 4.56 Å3/Da / Density % sol: 73.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97861 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97861 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 24776 / % possible obs: 99.1 % / Redundancy: 7 % / Biso Wilson estimate: 33.13 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.329 / Net I/av σ(I): 20.167 / Net I/σ(I): 5.5 / Num. measured all: 173456 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 4YN7 Resolution: 2.4→49.081 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.83 / 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: 106.64 Å2 / Biso mean: 38.897 Å2 / Biso min: 16.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→49.081 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: 7
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