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Yorodumi- PDB-6p8k: Escherichia coli Bacterioferritin Substituted with Zinc Protoporp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p8k | ||||||
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Title | Escherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Taylor, A.B. / Cioloboc, D. / Kurtz, D.M. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p8k.cif.gz | 967.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p8k.ent.gz | 721.7 KB | Display | PDB format |
PDBx/mmJSON format | 6p8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p8k_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
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Full document | 6p8k_full_validation.pdf.gz | 4.9 MB | Display | |
Data in XML | 6p8k_validation.xml.gz | 104 KB | Display | |
Data in CIF | 6p8k_validation.cif.gz | 147.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/6p8k ftp://data.pdbj.org/pub/pdb/validation_reports/p8/6p8k | HTTPS FTP |
-Related structure data
Related structure data | 6p8lC 2y3qS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-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 |
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-Non-polymers , 5 types, 2580 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ZNH / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-MLI / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.4 M sodium malonate, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.96 Å / Num. obs: 337873 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 19.43 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.048 / Rrim(I) all: 0.178 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 12.6 % / Rmerge(I) obs: 3.56 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 48968 / CC1/2: 0.48 / Rpim(I) all: 1.039 / Rrim(I) all: 3.71 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2Y3Q Resolution: 1.7→19.96 Å / SU ML: 0.2549 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 29.2534
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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