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Yorodumi- PDB-3hwg: Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hwg | ||||||
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Title | Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam-hopo2 | ||||||
Components | Neutrophil gelatinase-associated lipocalin | ||||||
Keywords | TRANSPORT PROTEIN / Lipocalin / siderophore / beta-barrel / Disulfide bond / Glycoprotein / Pyrrolidone carboxylic acid / Secreted | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Used previously-determined structure / Resolution: 2.19 Å | ||||||
Authors | Clifton, M.C. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hwg.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hwg.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/3hwg ftp://data.pdbj.org/pub/pdb/validation_reports/hw/3hwg | HTTPS FTP |
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-Related structure data
Related structure data | 3cmpC 3hwdC 3hweC 3hwfC 3i0aC 3k3lC 3tf6C 3tnyC 3tzsC 1l6mS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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 on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 22597.963 Da / Num. of mol.: 3 / Mutation: C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HNL, LCN2, NGAL / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P80188 |
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-Non-polymers , 7 types, 201 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.72 % |
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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: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 |
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: 2.19→50 Å / Num. all: 52918 / Num. obs: 40660 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 24.29 |
Reflection shell | Resolution: 2.19→2.28 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 6.6 / Num. unique all: 3989 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Used previously-determined structure Starting model: PDB ENTRY 1L6M Resolution: 2.19→46.93 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.553 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.212 / 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: 31.102 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→46.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.192→2.249 Å / Total num. of bins used: 20
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