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- PDB-3cmp: Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cmp | ||||||
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Title | Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin | ||||||
![]() | Neutrophil gelatinase-associated lipocalin | ||||||
![]() | ANTIMICROBIAL PROTEIN / Lipocalin / Siderocalin / Enterobactin / Siderophore / Iron / Glycoprotein / Pyrrolidone carboxylic acid / Secreted | ||||||
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. / Strong, R.K. | ||||||
![]() | ![]() 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 | ![]() | 120.2 KB | Display | ![]() |
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PDB format | ![]() | 90.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hwdC ![]() 3hweC ![]() 3hwfC ![]() 3hwgC ![]() 3i0aC ![]() 3k3lC ![]() 3tf6C ![]() 3tnyC ![]() 3tzsC ![]() 1l6mS 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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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: 1 / 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: 4 / Auth seq-ID: 5 - 177 / Label seq-ID: 25 - 197
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Details | C87S mutation disrupts dimer formation |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 22539.861 Da / Num. of mol.: 3 / Mutation: C87S, K125A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 113 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EB4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DBH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EB4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DBH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.2M Ammonium sulfate, 30% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→82.48 Å / Num. all: 20269 / Num. obs: 20066 / % possible obs: 99 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 29.85 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.92 / Num. unique all: 1955 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1L6M Resolution: 2.8→47.96 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.823 / SU B: 15.276 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R: 0.947 / ESU R Free: 0.407 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.185 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→47.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2255 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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