+Open data
-Basic information
Entry | Database: PDB / ID: 1dg1 | ||||||
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Title | WHOLE, UNMODIFIED, EF-TU(ELONGATION FACTOR TU). | ||||||
Components | ELONGATION FACTOR TUEF-Tu | ||||||
Keywords | RNA BINDING PROTEIN / ELONGATION FACTOR / TRNA BINDING / ALPHA BETA SHIFT / TS BINDING PROTEIN / GTPASE / GDP BINDING | ||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Abel, K. / Yoder, M. / Hilgenfeld, R. / Jurnak, F. | ||||||
Citation | Journal: Structure / Year: 1996 Title: An alpha to beta conformational switch in EF-Tu. Authors: Abel, K. / Yoder, M.D. / Hilgenfeld, R. / Jurnak, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dg1.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dg1.ent.gz | 129.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/1dg1 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/1dg1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer, Tu with a GDP substrate bound. |
-Components
#1: Protein | Mass: 43370.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CELL CYTOPLASM EXTRACT / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6N1, UniProt: P0CE48*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.75 Details: PEG 3350, ammonium citrate, ammonium acetate, pH 5.75, VAPOR DIFFUSION, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Mar 1, 1996 / Details: collimator |
Radiation | Monochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→63.123 Å / Num. all: 357998 / Num. obs: 28782 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.25 Å2 / Rsym value: 0.0613 |
Reflection | *PLUS Num. measured all: 357998 / Rmerge(I) obs: 0.0678 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.68 Å / % possible obs: 91 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 7 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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