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Open data
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Basic information
Entry | Database: PDB / ID: 6nal | ||||||
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Title | Crystal Structure of Gram Negative Toxin | ||||||
![]() | Thiol-activated cytolysin | ||||||
![]() | TOXIN / CYTOLYSIN | ||||||
Function / homology | ![]() HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Desulfobulbus propionicus | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morton, C.J. / Lawrence, S.A. / Parker, M.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Structural Basis for a Transition State That Regulates Pore Formation in a Bacterial Toxin. Authors: Wade, K.R. / Lawrence, S.L. / Farrand, A.J. / Hotze, E.M. / Kuiper, M.J. / Gorman, M.A. / Christie, M.P. / Panjikar, S. / Morton, C.J. / Parker, M.W. / Tweten, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 353.4 KB | Display | ![]() |
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PDB format | ![]() | 303.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.8 KB | Display | ![]() |
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Full document | ![]() | 482.4 KB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 52.8 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
#1: Protein | Mass: 53010.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 33891 / DSM 2032 / 1pr3 / Gene: Despr_1128 / Production host: ![]() ![]() #2: Chemical | ChemComp-PG4 / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.95 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG 6000, 10% Tacsimate pH 5.0 |
-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: Dec 9, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→44.98 Å / Num. obs: 61001 / % possible obs: 100 % / Redundancy: 35.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.049 / Rrim(I) all: 0.314 / Net I/σ(I): 11.4 / Num. measured all: 2147128 / Scaling rejects: 2403 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.49 Å2 / Biso mean: 59.2977 Å2 / Biso min: 22.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→43.445 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %
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