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- PDB-5uyt: Crystal structure of ice binding protein from an Antarctic bacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uyt | ||||||
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Title | Crystal structure of ice binding protein from an Antarctic bacterium Flavobacteriaceae | ||||||
![]() | Ice-binding protein | ||||||
![]() | ANTIFREEZE PROTEIN / ice binding protein / right-handed beta-helix / beta-solenoid | ||||||
Function / homology | Ice-binding protein / Ice-binding-like / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / NITRATE ION / Ice-binding protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, C. / Pakhomova, S. / Newcomer, M.E. / Christner, B.C. / Luo, B.-H. | ||||||
![]() | ![]() Title: Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein. Authors: Wang, C. / Pakhomova, S. / Newcomer, M.E. / Christner, B.C. / Luo, B.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 322.6 KB | Display | ![]() |
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PDB format | ![]() | 271.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.9 KB | Display | ![]() |
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Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 36 KB | Display | |
Data in CIF | ![]() | 54.7 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 52785.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: A bacterial antifreeze protein / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NO3 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / Details: 15-20% PEG 3350, 0.2 M ammonium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 2, 2012 / Details: Oxford Danfysik toroidal focusing mirror |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→36.08 Å / Num. obs: 101962 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.09 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 10103 / Rsym value: 0.732 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.613 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→36.08 Å
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Refine LS restraints |
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