+Open data
-Basic information
Entry | Database: PDB / ID: 1dar | ||||||
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Title | ELONGATION FACTOR G IN COMPLEX WITH GDP | ||||||
Components | ELONGATION FACTOR G | ||||||
Keywords | TRANSLATIONAL GTPASE / RIBOSOMAL TRANSLOCASE | ||||||
Function / homology | Function and homology information ribosome disassembly / translation elongation factor activity / GTPase activity / GTP binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Al-Karadaghi, S. / Aevarsson, A. / Garber, M. / Zheltonosova, J. / Liljas, A. | ||||||
Citation | Journal: Structure / Year: 1996 Title: The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange. Authors: al-Karadaghi, S. / Aevarsson, A. / Garber, M. / Zheltonosova, J. / Liljas, A. #1: Journal: Embo J. / Year: 1994 Title: Three-Dimensional Structure of the Ribosomal Translocase: Elongation Factor G from Thermus Thermophilus Authors: Aevarsson, A. / Brazhnikov, E. / Garber, M. / Zheltonosova, J. / Chirgadze, Y. / Al-Karadaghi, S. / Svensson, L.A. / Liljas, A. #2: Journal: Embo J. / Year: 1994 Title: The Crystal Structure of Elongation Factor G Complexed with Gdp, at 2.7 A Resolution Authors: Czworkowski, J. / Wang, J. / Steitz, T.A. / Moore, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dar.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dar.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dar_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 1dar_full_validation.pdf.gz | 480.8 KB | Display | |
Data in XML | 1dar_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1dar_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1dar ftp://data.pdbj.org/pub/pdb/validation_reports/da/1dar | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 76977.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN5 |
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#2: Chemical | ChemComp-GDP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.62 % | |||||||||||||||||||||||||
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Crystal grow | pH: 3 / Details: pH 3. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop / Details: Reshetnikova, L. S., (1983) FEBS Lett., 154, 149. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→10 Å / Num. obs: 32595 / % possible obs: 87 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 |
Reflection shell | Highest resolution: 2.4 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.9 / % possible all: 46 |
Reflection | *PLUS Num. measured all: 284145 |
Reflection shell | *PLUS % possible obs: 46 % |
-Processing
Software |
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Refinement | Resolution: 2.4→8 Å / σ(F): 0 Details: ATOMS WITH ZERO OCCUPANCY COULD NOT BE LOCATED IN THE ELECTRON DENSITY MAP. RESIDUES 39 - 66 (THE EFFECTOR LOOP) COULD NOT BE LOCALIZED IN THE ELECTRON DENSITY MAP. DOMAIN III (APPROXIMATELY ...Details: ATOMS WITH ZERO OCCUPANCY COULD NOT BE LOCATED IN THE ELECTRON DENSITY MAP. RESIDUES 39 - 66 (THE EFFECTOR LOOP) COULD NOT BE LOCALIZED IN THE ELECTRON DENSITY MAP. DOMAIN III (APPROXIMATELY RESIDUES 400 - 480) IS DISORDERED. SOME PARTS WERE MODELED AS POLYALANINE. THESE INCLUDE RESIDUES 433 - 442, 448 - 456, 466 - 476.
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22 / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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