[English] 日本語
Yorodumi- PDB-5i0v: IRON AND COPPER-BOUND P19 FROM CAMPYLOBACTER JEJUNI UNDER OXIDIZI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i0v | ||||||
---|---|---|---|---|---|---|---|
Title | IRON AND COPPER-BOUND P19 FROM CAMPYLOBACTER JEJUNI UNDER OXIDIZING CONDITIONS | ||||||
Components | Protein P19 | ||||||
Keywords | METAL TRANSPORT / MIXED BETA SANDWICH / IRON TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Campylobacter jejuni subsp. jejuni serotype O:23/36 (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Chan, A.C. / Murphy, M.E. | ||||||
Citation | Journal: Metallomics / Year: 2020 Title: A copper site is required for iron transport by the periplasmic proteins P19 and FetP. Authors: Chan, A.C.K. / Lin, H. / Koch, D. / Grass, G. / Nies, D.H. / Murphy, M.E.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5i0v.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5i0v.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 5i0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/5i0v ftp://data.pdbj.org/pub/pdb/validation_reports/i0/5i0v | HTTPS FTP |
---|
-Related structure data
Related structure data | 5i0wC 5i0xC 5i0yC 6wedC 6weeC 6wefC 3lzoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17590.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:23/36 (Campylobacter) Strain: 81-176 / Gene: CJJ81176_1650 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3PA01 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.14 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 25-45% PEG 350, 0.1M CHES PH 9 / PH range: 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→33.07 Å / Num. obs: 36846 / % possible obs: 100 % / Redundancy: 8.3 % / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LZO Resolution: 1.65→33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.887 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN USED IF PRESENT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.65 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|