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- PDB-5tcy: A complex of the synthetic siderophore analogue Fe(III)-5-LICAM w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tcy | ||||||
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Title | A complex of the synthetic siderophore analogue Fe(III)-5-LICAM with CeuE (H227L variant), a periplasmic protein from Campylobacter jejuni. | ||||||
![]() | Enterochelin uptake periplasmic binding protein | ||||||
![]() | METAL TRANSPORT / Periplasmic / Iron-Uptake / Tetradentate / Siderophore | ||||||
Function / homology | ![]() outer membrane-bounded periplasmic space / iron ion transport / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilde, E.J. / Blagova, E. / Hughes, A. / Raines, D.J. / Moroz, O.V. / Turkenburg, J.P. / Duhme-Klair, A.-K. / Wilson, K.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Interactions of the periplasmic binding protein CeuE with Fe(III) n-LICAM(4-) siderophore analogues of varied linker length. Authors: Wilde, E.J. / Hughes, A. / Blagova, E.V. / Moroz, O.V. / Thomas, R.P. / Turkenburg, J.P. / Raines, D.J. / Duhme-Klair, A.K. / Wilson, K.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.6 KB | Display | ![]() |
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PDB format | ![]() | 142.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5a5dC ![]() 5a5vC ![]() 5ad1C ![]() 5lwhC ![]() 5lwqC ![]() 5mbqC ![]() 5mbtC ![]() 5mbuC ![]() 3zkwS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32056.998 Da / Num. of mol.: 3 / Mutation: H227L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: K680_0601 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.33 % / Description: Rod shaped crystal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M PCB buffer, pH 8, 25% PEG 1500 +cryo 33% PEG 1500 in well solution |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2016 |
Radiation | Monochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→67.13 Å / Num. obs: 70811 / % possible obs: 95.9 % / Redundancy: 3.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.102 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.956 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.418 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZKW Resolution: 1.9→67.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.069 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.815 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→67.13 Å
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Refine LS restraints |
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