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- PDB-5kic: Long-sought stabilization of berkelium(IV) in solution: An anomal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kic | ||||||
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Title | Long-sought stabilization of berkelium(IV) in solution: An anomaly within the heavy actinide series | ||||||
![]() | Neutrophil gelatinase-associated lipocalin | ||||||
![]() | TRANSPORT PROTEIN / Siderophore-Binding / NGAL | ||||||
Function / homology | ![]() siderophore transport / Metal sequestration by antimicrobial proteins / enterobactin binding / iron ion sequestering activity / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding ...siderophore transport / Metal sequestration by antimicrobial proteins / enterobactin binding / iron ion sequestering activity / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding / innate immune response / apoptotic process / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rupert, P.B. / Strong, R.K. | ||||||
![]() | ![]() Title: Chelation and stabilization of berkelium in oxidation state +IV. Authors: Deblonde, G.J. / Sturzbecher-Hoehne, M. / Rupert, P.B. / An, D.D. / Illy, M.C. / Ralston, C.Y. / Brabec, J. / de Jong, W.A. / Strong, R.K. / Abergel, R.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 | ![]() | 228.5 KB | Display | ![]() |
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PDB format | ![]() | 185.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1l6mS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 3 - 177 / Label seq-ID: 5 - 179
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 20700.564 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 52 molecules 








#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: NaCl, Li2SO4,Acetate, Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 24695 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 42.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1L6M Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 23.496 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.651 / ESU R Free: 0.306 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.415 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→50 Å
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Refine LS restraints |
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