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Yorodumi- PDB-3tey: Crystal Structure of Anthrax Protective Antigen (Membrane Inserti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tey | ||||||
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Title | Crystal Structure of Anthrax Protective Antigen (Membrane Insertion Loop Deleted) Mutant S337C N664C to 2.06-A resolution | ||||||
Components | Protective antigen | ||||||
Keywords | protein transport / toxin | ||||||
Function / homology | Function and homology information positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / membrane ...positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / toxin activity / host cell plasma membrane / extracellular region / membrane / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Feld, G.K. / Krantz, B.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Domain flexibility modulates the heterogeneous assembly mechanism of anthrax toxin protective antigen. Authors: Feld, G.K. / Kintzer, A.F. / Tang, I.I. / Thoren, K.L. / Krantz, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tey.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tey.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/3tey ftp://data.pdbj.org/pub/pdb/validation_reports/te/3tey | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 80738.742 Da / Num. of mol.: 1 / Mutation: V303P,H304G,S337C,N664C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BXA0164, GBAA_pXO1_0164, pag, pagA, PX01, pXO1-110 / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): DE3(BL21) / References: UniProt: P13423*PLUS | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CLOSEST DATABASE REFERENCE TO THE CRYSTALLIZED SEQUENCE CORRESPONDS TO UNP ENTRY P13423, WHICH ...THE CLOSEST DATABASE REFERENCE TO THE CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.02 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% (15/4 EO/OH), 0.05M bis-tris-Cl, 0.05M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2010 |
Radiation | Monochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→25.06 Å / Num. all: 50702 / Num. obs: 50702 / % possible obs: 99.9 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 7.6 % / Biso Wilson estimate: 36.331 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.06→2.12 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3441 / Rsym value: 0.868 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→23.857 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 23.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.289 Å2 / ksol: 0.323 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.12→23.857 Å
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Refine LS restraints |
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LS refinement shell |
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