[English] 日本語
Yorodumi- PDB-4tog: 1.80A resolution structure of BfrB (C89S, K96C) crystal form 2 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tog | ||||||
---|---|---|---|---|---|---|---|
Title | 1.80A resolution structure of BfrB (C89S, K96C) crystal form 2 from Pseudomonas aeruginosa | ||||||
Components | Bacterioferritin | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / iron binding / iron mobilization | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Lovell, S. / Battaile, K.P. / Yao, H. / Kumar, R. / Eshelman, K. / Rivera, M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Authors: Yao, H. / Rui, H. / Kumar, R. / Eshelman, K. / Lovell, S. / Battaile, K.P. / Im, W. / Rivera, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4tog.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4tog.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 4tog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tog_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4tog_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4tog_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 4tog_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/4tog ftp://data.pdbj.org/pub/pdb/validation_reports/to/4tog | HTTPS FTP |
-Related structure data
Related structure data | 4to9C 4toaC 4tobC 4tocC 4todC 4toeC 4tofC 4tohC 3is7S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 6|||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 18538.066 Da / Num. of mol.: 4 / Mutation: C89S, K96C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bfrB, PA3531 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase |
---|
-Non-polymers , 6 types, 658 molecules
#2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-K / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | B205 LIES ON A 3-FOLDS AXIS, THE S AND O4 ATOMS ARE GENERATED BY THE SYMMETRY OPERATION -X+Y, -X+1, ...B205 LIES ON A 3-FOLDS AXIS, THE S AND O4 ATOMS ARE GENERATED BY THE SYMMETRY OPERATION -X+Y, -X+1, Z; 2)-Y+1, X-Y+1, Z |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Colour: Red prism / Density Matthews: 3.63 Å3/Da / Density % sol: 66.16 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 35% (v/v) MPD, 0.1M MES, 0.2M Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.8→48.27 Å / Num. obs: 101666 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 25.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.024 / Net I/σ(I): 20.8 / Num. measured all: 2015697 / Scaling rejects: 4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IS7 Resolution: 1.8→37.272 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 17.55 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.73 Å2 / Biso mean: 27.7453 Å2 / Biso min: 15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→37.272 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %
|