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Yorodumi- PDB-1b23: E. coli cysteinyl-tRNA and T. aquaticus elongation factor EF-TU:G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b23 | |||||||||
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Title | E. coli cysteinyl-tRNA and T. aquaticus elongation factor EF-TU:GTP ternary complex | |||||||||
Components |
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Keywords | GENE REGULATION/RNA / TRANSLATION ELONGATION FACTOR / TRANSFER RNA / PROTEIN SYNTHESIS / GENE REGULATION-RNA COMPLEX | |||||||||
Function / homology | Function and homology information translation elongation factor activity / GTPase activity / GTP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Thermus aquaticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Nissen, P. / Kjeldgaard, M. / Thirup, S. / Nyborg, J. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Authors: Nissen, P. / Thirup, S. / Kjeldgaard, M. / Nyborg, J. #1: Journal: Science / Year: 1995 Title: Crystal Structure of the Ternary Complex of Phe-tRNAphe, EF-TU, and a GTP Analog Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Polekhina, G. / Reshetnikova, L. / Clark, B.F.C. / Nyborg, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b23.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b23.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b23 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b23 | HTTPS FTP |
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-Related structure data
Related structure data | 1tttS S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
-RNA chain / Protein , 2 types, 2 molecules RP
#1: RNA chain | Mass: 23927.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: AMINOACYL LINK BETWEEN A76 AND CYS77 / Source: (gene. exp.) Escherichia coli (E. coli) |
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#2: Protein | Mass: 44742.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Strain: YT-1 / Gene: TUFA / Production host: Escherichia coli (E. coli) / References: UniProt: Q01698 |
-Non-polymers , 5 types, 268 molecules
#3: Chemical | #4: Chemical | ChemComp-CYS / | #5: Chemical | #6: Chemical | ChemComp-GNP / | #7: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 43 % / Description: ANISOTROPIC DIFFRACTION | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 2.1 M (NH4)2SO4, 30 MM TRIS, 5 MM MES, 10 MM MGCL2, 10 MM DTT, 1 MM GDPNP PH 6.7, 4 DEG. C, HANGING DROP, vapor diffusion - hanging drop, temperature 277K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.098 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.098 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 18435 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 33.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.396 / % possible all: 56 |
Reflection | *PLUS Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 56 % / Rmerge(I) obs: 0.396 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TTT Resolution: 2.6→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: ANISOTROPIC SCALING WAS CRUCIAL FOR REFINEMENT. ANISOTROPIC SCALEFACTORS DERIVED FROM 4.0 - 2.6 A AMPLITUDES THE ISOPENTENYL GROUP OF MIA R 37 AND THE N-TERMINAL ALA P 1 RESIDUE WERE STEREOCHEMICALLY MODELED
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Displacement parameters | Biso mean: 56.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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