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Open data
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Basic information
Entry | Database: PDB / ID: 5eb2 | |||||||||
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Title | Trp-bound YfiR | |||||||||
![]() | YfiR | |||||||||
![]() | TRANSCRIPTION / PERIPLASMIC REPRESSOR PROTEIN | |||||||||
Function / homology | YfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / TRYPTOPHAN / Negative regulator YfiR![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xu, M. / Yang, X. / Yang, X.-A. / Zhou, L. / Liu, T.-Z. / Fan, Z. / Jiang, T. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.5 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.8 KB | Display | ![]() |
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Full document | ![]() | 462.1 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eazC ![]() 5eb0C ![]() 5eb1C ![]() 5eb3C ![]() 4yn7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 17392.783 Da / Num. of mol.: 2 / Fragment: UNP residues 35-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-TRP / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M NaCl, 0.1 M BIS-TRIS, 25%(w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.7→50 Å / Num. obs: 18400 / % possible obs: 99.9 % / Redundancy: 28.7 % / Biso Wilson estimate: 32.23 Å2 / Rmerge(I) obs: 0.117 / Χ2: 0.981 / Net I/av σ(I): 28.721 / Net I/σ(I): 9.8 / Num. measured all: 527498 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YN7 Resolution: 2.709→41.535 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.55 / 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: 101.26 Å2 / Biso mean: 35.3738 Å2 / Biso min: 10.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.709→41.535 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: 6
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