+Open data
-Basic information
Entry | Database: PDB / ID: 2efg | ||||||
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Title | TRANSLATIONAL ELONGATION FACTOR G COMPLEXED WITH GDP | ||||||
Components |
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Keywords | PROTEIN BINDING / ELONGATION FACTOR / TRANSLOCASE / RIBOSOME / ELONGATION / TRANSLATION / PROTEIN SYNT FACTOR / GTPASE / GTP BINDING / GUANOSINE NUCLEOTIDE BINDING | ||||||
Function / homology | Function and homology information ribosome disassembly / translational elongation / translation elongation factor activity / GDP binding / ribosome binding / GTPase activity / GTP binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.6 Å | ||||||
Authors | Czworkowski, J. / Wang, J. / Steitz, T.A. / Moore, P.B. | ||||||
Citation | 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. #1: 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2efg.cif.gz | 136.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2efg.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 2efg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2efg_validation.pdf.gz | 796 KB | Display | wwPDB validaton report |
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Full document | 2efg_full_validation.pdf.gz | 813.3 KB | Display | |
Data in XML | 2efg_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 2efg_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2efg ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2efg | HTTPS FTP |
-Related structure data
Related structure data | 1efgSC 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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Unit cell |
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-Components
#1: Protein | Mass: 76963.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P13551, UniProt: Q5SHN5*PLUS |
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#2: Protein | Mass: 7507.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 |
#3: Chemical | ChemComp-GDP / |
#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: 3.08 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.8 Details: 18% W/V PEG8000, 20MM TRIS-HCL, 20MM AMMONIUM ACETATE, 2MM DTT, 1MM SODIUM AZIDE, 1MM GDP, pH 7.8, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 29, 1992 / Details: DOUBLE FOCUSING MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 29278 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 61.6 Å2 / Rsym value: 0.7 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.907 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: PDB ENTRY 1EFG Resolution: 2.6→80 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 7320367.21 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. REFINEMENT WAS THE MAXIMUM TARGET USING AMPLITUDES; REFINEMENT OF THIS STRUCTURE, LEADING TO ENTRY 1EFG, EMPLO PROGRAM X-PLOR
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.28 Å2 / ksol: 0.307 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→80 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 80 Å / σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 60.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.433 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.382 |