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- PDB-5uy4: YfeA from M9 minimal media supplemented with iron - Fe wavelength -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uy4 | ||||||
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Title | YfeA from M9 minimal media supplemented with iron - Fe wavelength | ||||||
![]() | 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 | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.3 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uxsC ![]() 5uxuC ![]() 5uy0SC ![]() 5uy5C ![]() 5uyaC ![]() 5uybC ![]() 5uycC ![]() 5uydC ![]() 5uyeC ![]() 5uyfC ![]() 5uygC ![]() 5uyhC ![]() 5uyvC ![]() 5uywC 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
#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-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.75 % / Description: tetragonal prism |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 30% PEG 4000, 20mM Bis-tris, 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: RAYONIX MX-300 / Detector: CCD / Date: Jan 10, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.74013 Å / Relative weight: 1 |
Reflection | Resolution: 1.915→50 Å / Num. obs: 21484 / % possible obs: 98 % / Redundancy: 7.9 % / Biso Wilson estimate: 27.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.024 / Net I/σ(I): 56 |
Reflection shell | Resolution: 1.915→1.95 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1046 / CC1/2: 0.934 / Rpim(I) all: 0.155 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5uy0 Resolution: 1.915→47.207 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.915→47.207 Å
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Refine LS restraints |
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LS refinement shell |
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