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Open data
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Basic information
Entry | Database: PDB / ID: 3rd0 | ||||||
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Title | Horse spleen apo-ferritin with bound thiopental | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / 4-HELIX BUNDLE / IRON / IRON STORAGE / METAL-BINDING | ||||||
Function / homology | ![]() : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() ![]() | ||||||
![]() | Oakley, S.H. / Vedula, L.S. / Xi, J. / Liu, R. / Eckenhoff, R.G. / Loll, P.J. | ||||||
![]() | ![]() Title: High resolution view of barbiturate recognition by a protein binding site Authors: Oakley, S.H. / Vedula, L.S. / Xi, J. / Liu, R. / Eckenhoff, R.G. / Loll, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.2 KB | Display | ![]() |
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PDB format | ![]() | 40 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.8 KB | Display | ![]() |
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Full document | ![]() | 459.3 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ravC ![]() 3f32S 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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Unit cell |
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Components
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | ChemComp-EDP / | ||||
#3: Chemical | ChemComp-CD / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2-1.6 M (NH4)2SO4 and 0.1-0.275 M CdSO4, 0.5 mM thiopental were mixed with equal volumes of apoferritin solution and equilibrated over 0.7-1 ml, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5498 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.79 Å / Num. all: 33846 / Num. obs: 33745 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 21.27 % / Biso Wilson estimate: 31.472 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 9.33 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.6 / % possible all: 97.3 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 43.1 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() ![]() Starting model: 3F32 without sidechains Resolution: 2→41.79 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.23 / σ(F): 0.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.755 Å2 / ksol: 0.399 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.84 Å2 / Biso mean: 28.736 Å2 / Biso min: 17.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2→41.79 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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