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Yorodumi- PDB-5uyb: YfeA from M9 minimal media supplemented with manganese - Fe wavelength -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uyb | ||||||
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Title | YfeA from M9 minimal media supplemented with manganese - Fe wavelength | ||||||
Components | Periplasmic chelated iron-binding protein YfeA | ||||||
Keywords | METAL TRANSPORT / polyspecific / transition metal / transport | ||||||
Function / homology | Function and homology information cellular response to iron ion / iron ion transport / periplasmic space / cell adhesion / metal ion binding Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Radka, C.D. / DeLucas, L.J. / Aller, S.G. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uyb.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uyb.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 5uyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/5uyb ftp://data.pdbj.org/pub/pdb/validation_reports/uy/5uyb | HTTPS FTP |
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-Related structure data
Related structure data | 5uxsC 5uxuC 5uy0C 5uy4C 5uy5C 5uyaSC 5uycC 5uydC 5uyeC 5uyfC 5uygC 5uyhC 5uyvC 5uywC 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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1 |
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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.) Yersinia pestis (bacteria) / Gene: yfeA, YPO2439, y1897, YP_2227 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56952 |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 27.79 % / Description: tetragonal prism |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.3 Details: 30% PEG 4000, 20mM Bis-tris propane, 50mM sodium chloride, 0.005% w/v sodium azide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.74013 Å |
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: 1.95→50 Å / Num. obs: 18617 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 22.293 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.035 / Net I/σ(I): 52.7 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 921 / CC1/2: 0.941 / Rpim(I) all: 0.158 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uya Resolution: 1.95→39.149 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→39.149 Å
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Refine LS restraints |
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LS refinement shell |
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