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- PDB-1dma: DOMAIN III OF PSEUDOMONAS AERUGINOSA EXOTOXIN COMPLEXED WITH NICO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dma | ||||||
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Title | DOMAIN III OF PSEUDOMONAS AERUGINOSA EXOTOXIN COMPLEXED WITH NICOTINAMIDE AND AMP | ||||||
![]() | EXOTOXIN A | ||||||
![]() | ADP-RIBOSYLATION | ||||||
Function / homology | ![]() NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Li, M. / Dyda, F. / Benhar, I. / Pastan, I. / Davies, D. | ||||||
![]() | ![]() 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. #1: ![]() Title: Functional Analysis of Domains II, Ib, and III of Pseudomonas Exotoxin Authors: Siegall, C.B. / Chaudhary, V.K. / Fitzgerald, D.J. / Pastan, I. #2: ![]() Title: Structure of Exotoxin a of Pseudomonas Aeruginosa a 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.9 KB | Display | ![]() |
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PDB format | ![]() | 68 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.9 KB | Display | ![]() |
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Full document | ![]() | 479.9 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 17.1 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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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 536 / 2: CIS PROLINE - PRO B 536 |
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Components
#1: Protein | Mass: 23334.041 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-AMP / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: used as seeds | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→8 Å / Num. obs: 16513 / % possible obs: 88.9 % / Observed criterion σ(I): 2 |
Reflection | *PLUS Rmerge(I) obs: 0.068 |
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Processing
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Refinement | Resolution: 2.5→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 32.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.264 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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