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- PDB-5uxu: YfeA from Yersinia pestis treated with EDTA during purification a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uxu | ||||||
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Title | YfeA from Yersinia pestis treated with EDTA during purification and crystallization | ||||||
![]() | Periplasmic chelated iron-binding protein YfeA | ||||||
![]() | METAL TRANSPORT / polyspecific / transition metal / transport | ||||||
Function / homology | ![]() cellular response to iron ion / iron ion transport / periplasmic space / cell adhesion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Radka, C.D. / DeLucas, L.J. / Aller, S.G. | ||||||
![]() | ![]() Title: Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites. Authors: Radka, C.D. / DeLucas, L.J. / Wilson, L.S. / Lawrenz, M.B. / Perry, R.D. / Aller, S.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80 KB | Display | ![]() |
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PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5uxsSC ![]() 5uy0C ![]() 5uy4C ![]() 5uy5C ![]() 5uyaC ![]() 5uybC ![]() 5uycC ![]() 5uydC ![]() 5uyeC ![]() 5uyfC ![]() 5uygC ![]() 5uyhC ![]() 5uyvC ![]() 5uywC S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 36048.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.31 % / Description: tetragonal prism |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 2mM EDTA, 30% PEG4000, 20mM Bis-tris propane, 50mM sodium chloride, 0.05% w/v sodium azide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28229 Å / Relative weight: 1 |
Reflection | Resolution: 1.839→50 Å / Num. obs: 26517 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.045 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.042 / Net I/σ(I): 48.9 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1199 / CC1/2: 0.924 / Rpim(I) all: 0.122 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5uxs Resolution: 1.839→40.846 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.02 / 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: 1.839→40.846 Å
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Refine LS restraints |
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LS refinement shell |
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