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Open data
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Basic information
Entry | Database: PDB / ID: 5zu4 | ||||||
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Title | Crystal structure of Lamprey immune protein | ||||||
![]() | Natterin-like protein | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, Q.W. / Pang, Y. | ||||||
![]() | ![]() Title: Structure of a pore-forming protein Authors: Li, Q.W. / Pang, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.5 KB | Display | ![]() |
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PDB format | ![]() | 106 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6iulC ![]() 4nzoS S: Starting model for refinement 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34340.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 157 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / ![]() #3: Chemical | ChemComp-CL / ![]() #4: Chemical | ChemComp-GOL / ![]() #5: Chemical | ChemComp-PEG / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.56 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1,4-Dioxane, Polyethylene glycol 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.25→89.08 Å / Num. obs: 41118 / % possible obs: 99.9 % / Redundancy: 16 % / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 2.25→2.29 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4NZO Resolution: 2.39→89.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.38 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.227 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.27 Å2 / Biso mean: 52.299 Å2 / Biso min: 25.98 Å2
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Refinement step | Cycle: final / Resolution: 2.39→89.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.389→2.451 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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