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Yorodumi- PDB-3tew: Crystal Structure of Anthrax Protective Antigen (Membrane Inserti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tew | ||||||
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Title | Crystal Structure of Anthrax Protective Antigen (Membrane Insertion Loop Deleted) to 1.45-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: 1.45 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 | 3tew.cif.gz | 307.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tew.ent.gz | 247.9 KB | Display | PDB format |
PDBx/mmJSON format | 3tew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/3tew ftp://data.pdbj.org/pub/pdb/validation_reports/te/3tew | HTTPS FTP |
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-Related structure data
Related structure data | 3texC 3teyC 3tezC 1accS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 80733.641 Da / Num. of mol.: 1 / Mutation: V303P,H304G 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: Chemical | #4: 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: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG-ME 2000, 0.1M Tris-Cl, 0.2M Trimethylamine-N-oxide, pH 8.5, 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: Oct 7, 2009 |
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: 1.45→23 Å / Num. all: 126263 / Num. obs: 126263 / % possible obs: 90.3 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 6.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.9 / Num. unique all: 7983 / Rsym value: 0.748 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ACC Resolution: 1.45→23 Å / SU ML: 0.19 / σ(F): 0.06 / Phase error: 22.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.37 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.323 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.45→23 Å
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Refine LS restraints |
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LS refinement shell |
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