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- PDB-5khp: Tightening the Recognition of Tetravalent Zr and Th Complexes by ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5khp | ||||||
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Title | Tightening the Recognition of Tetravalent Zr and Th Complexes by the Siderophore-Binding Mammalian Protein Siderocalin for Theranostic Applications | ||||||
![]() | Neutrophil gelatinase-associated lipocalin | ||||||
![]() | METAL BINDING PROTEIN / Siderophore-Binding / NGAL | ||||||
Function / homology | ![]() siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / 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 / iron ion sequestering activity / enterobactin binding / 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 / Neutrophil degranulation / apoptotic process / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rupert, P.B. / Strong, R.K. | ||||||
![]() | ![]() Title: Engineered Recognition of Tetravalent Zirconium and Thorium by Chelator-Protein Systems: Toward Flexible Radiotherapy and Imaging Platforms. Authors: Captain, I. / Deblonde, G.J. / Rupert, P.B. / An, D.D. / Illy, M.C. / Rostan, E. / Ralston, C.Y. / 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 | ![]() | 222 KB | Display | ![]() |
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PDB format | ![]() | 176.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5kidC ![]() 1lm6S 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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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: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 20700.564 Da / Num. of mol.: 3 / Fragment: UNP residues 21-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 68 molecules ![](data/chem/img/ZR.gif)
![](data/chem/img/7K9.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/7K9.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: Acetate, Li2SO4, NaCl, ammonium Sulphate |
-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: 2.65→50 Å / Num. obs: 22217 / % possible obs: 95.4 % / Redundancy: 8.1 % / Net I/σ(I): 28.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LM6 Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.916 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.573 / ESU R Free: 0.28 / 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: 54.645 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→50 Å
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Refine LS restraints |
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