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- PDB-8bgm: Crystal structure of the OrfX1-OrfX3 complex from the PMP1 neurot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bgm | |||||||||
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Title | Crystal structure of the OrfX1-OrfX3 complex from the PMP1 neurotoxin gene cluster | |||||||||
![]() | (Toxin![]() | |||||||||
![]() | ![]() | |||||||||
Function / homology | Clostridium P47 protein / Clostridium P-47 protein / membrane => GO:0016020 / ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kosenina, S. / Stenmark, P. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Crystal structure of the OrfX1-OrfX3 complex from the PMP1 neurotoxin gene cluster. Authors: Kosenina, S. / Stenmark, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 245.7 KB | Display | ![]() |
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PDB format | ![]() | 196.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | ![]() Mass: 18546.389 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: OrfX1 Source: (gene. exp.) ![]() ![]() Gene: D4A35_18135 / Production host: ![]() ![]() ![]() #2: Protein | ![]() Mass: 55052.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: OrfX3 Source: (gene. exp.) ![]() ![]() Gene: D4A35_18125 / Production host: ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.66 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→77.1 Å / Num. obs: 50841 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.06 / Rrim(I) all: 0.16 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4574 / CC1/2: 0.742 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Alphafold model Resolution: 2.7→63.367 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.219 / Average fsc free: 0.7891 / Average fsc work: 0.7991 / Cross valid method: FREE R-VALUE / ESU R: 0.622 / ESU R Free: 0.324 / Details: Hydrogens have not been used
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.008 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→63.367 Å
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Refine LS restraints |
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LS refinement shell |
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