[English] 日本語
Yorodumi- PDB-6p8l: Escherichia coli Bacterioferritin Substituted with Zinc Protoporp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p8l | ||||||
---|---|---|---|---|---|---|---|
Title | Escherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-ray Data) | ||||||
Components | Bacterioferritin | ||||||
Keywords | METAL BINDING PROTEIN / OXIDOREDUCTASE / bacterioferritin / zinc protoporphyrin IX / photosensitizer / ferritin | ||||||
Function / homology | Function and homology information iron ion sequestering activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...iron ion sequestering activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Taylor, A.B. / Cioloboc, D. / Kurtz, D.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2020 Title: Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction. Authors: Benavides, B.S. / Valandro, S. / Cioloboc, D. / Taylor, A.B. / Schanze, K.S. / Kurtz Jr., D.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6p8l.cif.gz | 484.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6p8l.ent.gz | 370.7 KB | Display | PDB format |
PDBx/mmJSON format | 6p8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p8l_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6p8l_full_validation.pdf.gz | 4.3 MB | Display | |
Data in XML | 6p8l_validation.xml.gz | 92.5 KB | Display | |
Data in CIF | 6p8l_validation.cif.gz | 125.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/6p8l ftp://data.pdbj.org/pub/pdb/validation_reports/p8/6p8l | HTTPS FTP |
-Related structure data
Related structure data | 6p8kSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 18518.016 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: bfr, b3336, JW3298 / Plasmid: pCV3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABD3, ferroxidase |
---|
-Non-polymers , 5 types, 1645 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-MLI / #5: Chemical | ChemComp-ZNH / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.75 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.4 M sodium malonate, pH 6.0 |
-Data collection
Diffraction |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||||||||||||
Detector |
| ||||||||||||||||||||||||||||||
Radiation |
| ||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||
Reflection | Entry-ID: 6P8L / CC1/2: 0.998 / % possible obs: 99.8 %
| ||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 6P8K Resolution: 2.1→92.65 Å / SU ML: 0.2974 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.7513
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→92.65 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|