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Open data
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Basic information
Entry | Database: PDB / ID: 2ip6 | ||||||
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Title | Crystal structure of PedB | ||||||
![]() | PapB | ||||||
![]() | ANTIMICROBIAL PROTEIN / immunity protein to the pediocin PP-1 | ||||||
Function / homology | de novo design (two linked rop proteins) - #140 / Lactococcin-A immunity protein-like / Enterocin A Immunity / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / Immunity protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kang, S.O. / Kim, I.K. / Kim, M.K. / Kim, J.H. / Yim, H.S. / Cha, S.S. | ||||||
![]() | ![]() Title: High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins Authors: Kim, I.K. / Kim, M.K. / Kim, J.H. / Yim, H.S. / Cha, S.S. / Kang, S.O. #1: Journal: Biochim.Biophys.Acta / Year: 2005 Title: Crystallization and preliminary X-ray crystallographic analysis of the pediocin immunity protein (PedB) from Pediococcus pentosaceus at 1.35 A resolution Authors: Kim, I.K. / Kim, M.K. / Yim, H.S. / Cha, S.S. / Kang, S.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.2 KB | Display | ![]() |
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PDB format | ![]() | 21.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.8 KB | Display | ![]() |
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Full document | ![]() | 441.9 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 13011.685 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.711271 Å3/Da / Density % sol: 28.123611 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 6 Details: 2.4M ammonium sulfate, 0.3M sodium chloride, 0.1M MES, pH 6.0, EVAPORATION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() | ||||||||||||
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: Apr 2, 2005 | ||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.35→30 Å / Num. all: 19433 / Num. obs: 18937 / % possible obs: 97.4 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 | ||||||||||||
Reflection shell | Resolution: 1.35→1.4 Å / Mean I/σ(I) obs: 2.6 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.8088 Å2 / ksol: 0.358512 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.35→18.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.43 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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