+Open data
-Basic information
Entry | Database: PDB / ID: 6nal | ||||||
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Title | Crystal Structure of Gram Negative Toxin | ||||||
Components | Thiol-activated cytolysin | ||||||
Keywords | TOXIN / CYTOLYSIN | ||||||
Function / homology | Function and homology information 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 | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Morton, C.J. / Lawrence, S.A. / Parker, M.W. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Mbio / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nal.cif.gz | 353.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nal.ent.gz | 303.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nal_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 6nal_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 6nal_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 6nal_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/6nal ftp://data.pdbj.org/pub/pdb/validation_reports/na/6nal | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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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.) Desulfobulbus propionicus (strain ATCC 33891 / DSM 2032 / 1pr3) (bacteria) Strain: ATCC 33891 / DSM 2032 / 1pr3 / Gene: Despr_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: E8RGW2, UniProt: A0A7U3YL07*PLUS #2: Chemical | ChemComp-PG4 / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372, 0.97902, 0.97957 | ||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→43.445 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.58
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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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