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Open data
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Basic information
Entry | Database: PDB / ID: 7pfi | ||||||
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Title | 20 minute Fe2+ soaked structure of SynFtn Variant D65A | ||||||
![]() | Ferritin | ||||||
![]() | METAL BINDING PROTEIN / iron binding protein | ||||||
Function / homology | ![]() bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | structure determined from crystals of SynFtn D65A that have not been soaked in Fe2+ | ||||||
![]() | Hemmings, A.M. / Bradley, J.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Key carboxylate residues for iron transit through the prokaryotic ferritin Syn Ftn. Authors: Bradley, J.M. / Fair, J. / Hemmings, A.M. / Le Brun, N.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.4 KB | Display | ![]() |
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PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 971 KB | Display | ![]() |
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Full document | ![]() | 971.3 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pf7C ![]() 7pf8C ![]() 7pf9C ![]() 7pfbC ![]() 7pfgC ![]() 7pfhC ![]() 7pfjC ![]() 7pfkC ![]() 5ouwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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
#1: Protein | Mass: 20188.346 Da / Num. of mol.: 1 / Fragment: ferritin / Mutation: D65A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CC9311 / Gene: sync_1539 / Plasmid: pET21a / Production host: ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.57 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.64→53.19 Å / Num. obs: 29360 / % possible obs: 100 % / Redundancy: 78.5 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.008 / Rrim(I) all: 0.067 / Net I/σ(I): 46.5 / Num. measured all: 2303633 / Scaling rejects: 30 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OUW Resolution: 1.7→40.469 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.47 Å2 / Biso mean: 31.2947 Å2 / Biso min: 21.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→40.469 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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