+Open data
-Basic information
Entry | Database: PDB / ID: 1y9u | ||||||
---|---|---|---|---|---|---|---|
Title | Bordetella ferric binding protein | ||||||
Components | putative iron binding proteinIron-binding proteins | ||||||
Keywords | METAL BINDING PROTEIN / periplasmic binding protein / iron tyrosinate interaction | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Iron binding protein Function and homology information | ||||||
Biological species | Bordetella pertussis Tohama I (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Tom-Yew, S.A.L. / Cui, D.T. / Bekker, E.G. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Anion-independent iron coordination by the Campylobacter jejuni ferric binding protein Authors: Tom-Yew, S.A.L. / Cui, D.T. / Bekker, E.G. / Murphy, M.E.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1y9u.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1y9u.ent.gz | 111.9 KB | Display | PDB format |
PDBx/mmJSON format | 1y9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/1y9u ftp://data.pdbj.org/pub/pdb/validation_reports/y9/1y9u | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is the monomer |
-Components
#1: Protein | Mass: 34821.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria) Species: Bordetella pertussis / Strain: Tohama I / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7VXW9 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 1500, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Type: SSRL / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 2002 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→23.7 Å / Num. all: 59653 / Num. obs: 59653 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.4→1.42 Å / % possible all: 71.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→23.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.828 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.185 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→23.7 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.387→1.423 Å / Total num. of bins used: 20 /
|