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- PDB-3tny: Structure of YfiY from Bacillus cereus bound to the siderophore i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tny | ||||||
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Title | Structure of YfiY from Bacillus cereus bound to the siderophore iron (III) schizokinen | ||||||
![]() | YfiY (ABC transport system substrate-binding protein) | ||||||
![]() | METAL TRANSPORT / schizokinen / bacillus cereus / nutrient binding protein / ABC transporter | ||||||
Function / homology | Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-SKZ / : ![]() | ||||||
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 | ![]() | 77.5 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3cmpC ![]() 3hwdC ![]() 3hweC ![]() 3hwfC ![]() 3hwgC ![]() 3i0aC ![]() 3k3lC ![]() 3tf6C ![]() 3tzsC 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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Unit cell |
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Components
#1: Protein | Mass: 34460.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SKZ / [ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 312 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein 10-20 mg/ml, 0.1M HEPES 7.0, 30% Jeffamine ED-2001. Direct cryoprotection. , VAPOR DIFFUSION, HANGING DROP, temperature 312K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2010 |
Radiation | Monochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 46458 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.118 / Χ2: 0.949 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.55→1.61 Å / Χ2: 1.001 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 56.47 Å2 / Biso mean: 21.1498 Å2 / Biso min: 12.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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