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Yorodumi- PDB-1aer: DOMAIN III OF PSEUDOMONAS AERUGINOSA EXOTOXIN COMPLEXED WITH BETA-TAD -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aer | ||||||
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Title | DOMAIN III OF PSEUDOMONAS AERUGINOSA EXOTOXIN COMPLEXED WITH BETA-TAD | ||||||
Components | EXOTOXIN A | ||||||
Keywords | ADP-RIBOSYLATION / TOXIN / TRANSFERASE / GLYCOSYLTRANSFERASE / NAD | ||||||
Function / homology | Function and homology information NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Li, M. / Dyda, F. / Benhar, I. / Pastan, I. / Davies, D.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analog: implications for the activation process and for ADP ribosylation Authors: Li, M. / Dyda, F. / Benhar, I. / Pastan, I. / Davies, D.R. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: The Crystal Structure of Pseudomonas Aeruginosa Exotoxin Domain III with Nicotinamide and AMP: Conformational Differences with the Intact Exotoxin Authors: Li, M. / Dyda, F. / Benhar, I. / Pastan, I. / Davies, D.R. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986 Title: Structure of Exotoxin a of Pseudomonas Aeruginosa at 3.0-Angstrom Resolution Authors: Allured, V.S. / Collier, R.J. / Carroll, S.F. / Mckay, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aer.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aer.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 1aer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aer_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1aer_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1aer_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1aer_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/1aer ftp://data.pdbj.org/pub/pdb/validation_reports/ae/1aer | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22918.580 Da / Num. of mol.: 2 / Fragment: DOMAIN III OF PSEUDOMONAS TOXIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PPED5-399 / Production host: Escherichia coli (E. coli) References: UniProt: P11439, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-TAD / | #3: Chemical | ChemComp-TIA / | #4: Chemical | ChemComp-AMP / | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IN THIS ENTRY IS FROM 400 TO 613 FROM THAT OF THE COMPLETE TOXIN IN GENE BANK. THERE ...THE SEQUENCE IN THIS ENTRY IS FROM 400 TO 613 FROM THAT OF THE COMPLETE TOXIN IN GENE BANK. THERE ARE TWO MONOMERS IN THE ASYMMETRIC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 50.2 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 22417 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.057 |
Reflection | *PLUS % possible obs: 93.4 % / Redundancy: 4.7 % |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 78.4 % |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 28.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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