+Open data
-Basic information
Entry | Database: PDB / ID: 1ikq | ||||||
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Title | Pseudomonas Aeruginosa Exotoxin A, wild type | ||||||
Components | EXOTOXIN A | ||||||
Keywords | TRANSFERASE / DOMAIN I / II / III of EXOTOXIN A | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | McKay, D.B. / Wedekind, J.E. / Trame, C.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Refined Crystallographic Structure of Pseudomonas aeruginosa Exotoxin A and its Implications for the Molecular Mechanism of Toxicity Authors: Wedekind, J.E. / Trame, C.B. / Dorywalska, M. / Koehl, P. / Raschke, T.M. / McKee, M. / FitzGerald, D. / Collier, R.J. / McKay, D.B. #1: Journal: J.Mol.Biol. / Year: 1982 Title: Crystallization of Exotoxin A from Pseudomonas aeruginosa Authors: Collier, R.J. / McKay, D.B. #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. #3: Journal: Proteins / Year: 1988 Title: Mapping the Enzymatic Active Site of Pseudomonas aeruginosa Exotoxin A Authors: Brandhuber, B.J. / Allured, V.S. / G., Falbel T. / B., McKay D. #4: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ikq.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ikq.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ikq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ikq_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 1ikq_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 1ikq_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 1ikq_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/1ikq ftp://data.pdbj.org/pub/pdb/validation_reports/ik/1ikq | HTTPS FTP |
-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: 66871.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PE / Plasmid: pMOA1A2VK352 f+ T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P11439, Transferases; Glycosyltransferases; Pentosyltransferases | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, sodium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
Crystal grow | *PLUS Details: Collier, R.J., (1982) J. Mol. Biol., 157, 413. |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.62→50 Å / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.4 Å2 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 80328 / % possible obs: 93 % / Num. measured all: 224879 / Rmerge(I) obs: 0.04 | ||||||||||||||||||
Reflection shell | *PLUS Highest resolution: 1.62 Å / Lowest resolution: 1.71 Å / % possible obs: 91 % / Rmerge(I) obs: 0.185 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A EXOTOXIN A model (ref. 3) Resolution: 1.62→49.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1832154.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.8 Å2 / ksol: 0.369 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.62→49.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.69 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Num. reflection obs: 73810 / σ(F): 0 / % reflection Rfree: 8.1 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.286 / Rfactor obs: 0.286 |