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Open data
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Basic information
Entry | Database: PDB / ID: 5civ | ||||||
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Title | Sibling Lethal Factor Precursor - DfsB | ||||||
![]() | Sibling bacteriocin | ||||||
![]() | UNKNOWN FUNCTION / Bacteriocin / sporulation / DUF1706 / cell cycle | ||||||
Function / homology | Protein of unknown function DUF1706 / Protein of unknown function (DUF1706) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Sibling bacteriocin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Taylor, J.D. / Matthews, S.J. | ||||||
![]() | ![]() Title: Structures of the DfsB Protein Family Suggest a Cationic, Helical Sibling Lethal Factor Peptide. Authors: Taylor, J.D. / Taylor, G. / Hare, S.A. / Matthews, S.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 | ![]() | 50.2 KB | Display | ![]() |
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PDB format | ![]() | 38.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 406 KB | Display | ![]() |
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Full document | ![]() | 406.8 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 21868.219 Da / Num. of mol.: 1 / Fragment: residues 13-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dfsB / Plasmid: pQE-30 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 12% PEG 550 MME, 6% PEG 20,000, 0.1 M Sodium formate; 0.1 M Ammonium acetate; 0.1 M Sodium citrate tribasic dihydrate; 0.1 M Sodium potassium tartrate tetrahydrate; 0.1 M Sodium oxamate, 0.1 M Tris, 0.1 M Bicine PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2011 |
Radiation | Monochromator: 0.9788 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→21.51 Å / Num. obs: 32427 / % possible obs: 94.72 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.38→1.42 Å / Redundancy: 4.4 % / % possible all: 74.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.384→21.509 Å
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Refine LS restraints |
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LS refinement shell |
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