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- PDB-4zl5: Crystal structure of the PmFTN variant E44H soaked in iron (45 min) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zl5 | ||||||
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Title | Crystal structure of the PmFTN variant E44H soaked in iron (45 min) | ||||||
![]() | Ferritin | ||||||
![]() | OXIDOREDUCTASE / ferritin / di-iron ferroxidase centre / 4-helix bundle | ||||||
Function / homology | ![]() ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | 45 min soaked | ||||||
![]() | Pfaffen, S. / Murphy, M.E.P. | ||||||
![]() | ![]() Title: A Diatom Ferritin Optimized for Iron Oxidation but Not Iron Storage. Authors: Pfaffen, S. / Bradley, J.M. / Abdulqadir, R. / Firme, M.R. / Moore, G.R. / Le Brun, N.E. / Murphy, M.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 | ![]() | 220.6 KB | Display | ![]() |
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PDB format | ![]() | 176.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.5 KB | Display | ![]() |
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Full document | ![]() | 492.5 KB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 62.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zkhSC ![]() 4zkwC ![]() 4zkxC ![]() 4zl6C ![]() 4zlwC ![]() 4zmcC S: Starting model for refinement C: citing same article ( |
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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: 18975.146 Da / Num. of mol.: 6 / Mutation: E44H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodiaum acetate pH 5.5, Ammonium sulfate, NaCl / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.7 % / Number: 789488 / Rsym value: 0.083 / D res high: 1.85 Å / D res low: 170.31 Å / Num. obs: 117178 / % possible obs: 99.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.85→47.93 Å / Num. all: 117178 / Num. obs: 117178 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Rsym value: 0.083 / Net I/av σ(I): 6.578 / Net I/σ(I): 12 / Num. measured all: 789488 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZKH Resolution: 1.85→47.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2028 / WRfactor Rwork: 0.1679 / FOM work R set: 0.8637 / SU B: 2.757 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1068 / SU Rfree: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.54 Å2 / Biso mean: 29.158 Å2 / Biso min: 6.9 Å2
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Refinement step | Cycle: final / Resolution: 1.85→47.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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