[English] 日本語
Yorodumi- PDB-5uyc: YfeA from M9 minimal media supplemented with manganese - Mn wavelength -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uyc | ||||||
---|---|---|---|---|---|---|---|
Title | YfeA from M9 minimal media supplemented with manganese - Mn 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: 1.959 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5uyc.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5uyc.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 5uyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/5uyc ftp://data.pdbj.org/pub/pdb/validation_reports/uy/5uyc | HTTPS FTP |
---|
-Related structure data
Related structure data | 5uxsC 5uxuC 5uy0C 5uy4C 5uy5C 5uyaSC 5uybC 5uydC 5uyeC 5uyfC 5uygC 5uyhC 5uyvC 5uywC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.7 Å3/Da / Density % sol: 27.65 % / Description: tetragonal prism |
---|---|
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% sodium azide |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.89289 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: 1.89289 Å / Relative weight: 1 |
Reflection | Resolution: 1.959→50 Å / Num. obs: 18167 / % possible obs: 98.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 26.003 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.036 / Net I/σ(I): 73.2 |
Reflection shell | Resolution: 1.959→1.99 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 13.3 / Num. unique obs: 784 / CC1/2: 0.747 / Rpim(I) all: 0.208 / % possible all: 88.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uya Resolution: 1.959→38.286 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.07
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.959→38.286 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|