+Open data
-Basic information
Entry | Database: PDB / ID: 1zm9 | ||||||
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Title | Structure of eEF2-ETA in complex with PJ34 | ||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN/TRANSFERASE / elongation factor / toxin / ADP-ribosylation / BIOSYNTHETIC PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / nucleotidyltransferase activity ...NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / nucleotidyltransferase activity / maintenance of translational fidelity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome binding / toxin activity / protein-folding chaperone binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Joergensen, R. / Merrill, A.R. / Yates, S.P. / Marquez, V.E. / Schwan, A.L. / Boesen, T. / Andersen, G.R. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Authors: Joergensen, R. / Merrill, A.R. / Yates, S.P. / Marquez, V.E. / Schwan, A.L. / Boesen, T. / Andersen, G.R. | ||||||
History |
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Remark 600 | HETEROGEN P34 700 is associated with exotoxin A in chain B. P34 701 is associated with exotoxin A ...HETEROGEN P34 700 is associated with exotoxin A in chain B. P34 701 is associated with exotoxin A in chain D. P34 702 is associated with exotoxin A in chain F. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zm9.cif.gz | 593.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zm9.ent.gz | 482.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zm9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1zm9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1zm9_validation.xml.gz | 121.8 KB | Display | |
Data in CIF | 1zm9_validation.cif.gz | 162.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/1zm9 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/1zm9 | HTTPS FTP |
-Related structure data
Related structure data | 1zm2C 1zm3C 1zm4C 1aerS 1n0uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is one molecule of eEF2 and one molecule of ETA |
-Components
#1: Protein | Mass: 93549.320 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324 #2: Protein | Mass: 22496.010 Da / Num. of mol.: 3 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) References: GenBank: 151216, UniProt: P11439*PLUS, NAD+-diphthamide ADP-ribosyltransferase #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 6000, MPD, HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 104181 / Num. obs: 103348 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.108 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.8→3.15 Å / Redundancy: 3.7 % / Rsym value: 0.391 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entries 1n0u and 1aer Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: A699, C699 and E699 are MODELLED AS His, since diphthamide modification was disordered.
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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