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- PDB-3k3l: Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k3l | ||||||
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Title | Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with apo Enterobactin | ||||||
![]() | Neutrophil gelatinase-associated lipocalin | ||||||
![]() | TRANSPORT PROTEIN / NGAL / p25 / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Disulfide bond / Glycoprotein / Secreted / Siderocalin / beta-barrel / siderophore / enterobactin | ||||||
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 / apoptotic process / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Clifton, M.C. | ||||||
![]() | ![]() Title: Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands Authors: Clifton, M.C. / Rupert, P.B. / Hoette, T.M. / Raymond, K.N. / Abergel, R.J. / Strong, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.8 KB | Display | ![]() |
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PDB format | ![]() | 87.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 889 KB | Display | ![]() |
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Full document | ![]() | 896.9 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cmpC ![]() 3hwdC ![]() 3hweC ![]() 3hwfC ![]() 3hwgC ![]() 3i0aC ![]() 3tf6C ![]() 3tnyC ![]() 3tzsC ![]() 3ioa 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 20556.438 Da / Num. of mol.: 3 / Mutation: C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 131 molecules ![](data/chem/img/DBS.gif)
![](data/chem/img/DBH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MCK.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DBH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MCK.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DBS / | ||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-MCK / | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.62→50 Å / Num. all: 44579 / Num. obs: 23965 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 50.3 |
Reflection shell | Resolution: 2.62→2.7 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 7.51 / Num. unique all: 2347 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: Used previously-determined structure Resolution: 2.62→41.25 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.854 / SU B: 11.023 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.575 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.449 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→41.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.623→2.691 Å / Total num. of bins used: 20
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