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Yorodumi- PDB-5tcy: A complex of the synthetic siderophore analogue Fe(III)-5-LICAM w... -
+Open data
-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. | ||||||
Components | Enterochelin uptake periplasmic binding protein | ||||||
Keywords | METAL TRANSPORT / Periplasmic / Iron-Uptake / Tetradentate / Siderophore | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Campylobacter jejuni BJ-CJGB96299 (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | 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 | United Kingdom, 1items
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Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tcy.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tcy.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 5tcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/5tcy ftp://data.pdbj.org/pub/pdb/validation_reports/tc/5tcy | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Campylobacter jejuni BJ-CJGB96299 (Campylobacter) Gene: K680_0601 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W8LI20, UniProt: Q0P8Q4*PLUS #2: Chemical | #3: Chemical | #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: 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: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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