+Open data
-Basic information
Entry | Database: PDB / ID: 1ikp | ||||||
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Title | Pseudomonas Aeruginosa Exotoxin A, P201Q, W281A mutant | ||||||
Components | EXOTOXIN A | ||||||
Keywords | TRANSFERASE / all 3 EXOTOXIN A domains | ||||||
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: 1.45 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. / Falbel, T.G. / McKay, D.B. #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 | 1ikp.cif.gz | 140.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ikp.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ikp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ikp_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 1ikp_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 1ikp_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 1ikp_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/1ikp ftp://data.pdbj.org/pub/pdb/validation_reports/ik/1ikp | 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: 66787.820 Da / Num. of mol.: 1 / Mutation: W281A, P201Q 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.37 % |
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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 281.0K |
Crystal grow | *PLUS Details: Collier, R.J., (1982) J. Mol. Biol., 157, 413. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2000 / Details: double crystal monochromator |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→59.76 Å / Num. all: 293233 / Num. obs: 116635 / % possible obs: 88.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.52 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 5.8 / Num. unique all: 3860 / Rsym value: 0.117 / % possible all: 58 |
Reflection | *PLUS Lowest resolution: 60 Å / Num. measured all: 293233 |
Reflection shell | *PLUS % possible obs: 58 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Wild Type EXOTOXIN A, 1.62A Resolution: 1.45→21.82 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 12268844.2 / 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: 45.2689 Å2 / ksol: 0.373386 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.45→21.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.52 Å / Rfactor Rfree error: 0.009 / 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: 60 Å / Num. reflection obs: 97274 / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.299 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.27 / Rfactor obs: 0.27 |