+Open data
-Basic information
Entry | Database: PDB / ID: 1fnm | ||||||
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Title | STRUCTURE OF THERMUS THERMOPHILUS EF-G H573A | ||||||
Components | ELONGATION FACTOR G | ||||||
Keywords | TRANSLATION / Bent conformation / Visible domain III / Mutation His573Ala | ||||||
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 / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Laurberg, M. / Kristensen, O. / Martemyanov, K. / Gudkov, A.T. / Nagaev, I. / Hughes, D. / Liljas, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site. Authors: Laurberg, M. / Kristensen, O. / Martemyanov, K. / Gudkov, A.T. / Nagaev, I. / Hughes, D. / Liljas, A. #1: 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. #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. #3: 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. #4: Journal: FEBS Lett. / Year: 1998 Title: An Intact Conformation at the Tip of Elongation Factor G Domain IV is Functionally Important Authors: Martemyanov, K.A. / Yarunin, A.S. / Liljas, A. / Gudkov, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fnm.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fnm.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fnm_validation.pdf.gz | 736.5 KB | Display | wwPDB validaton report |
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Full document | 1fnm_full_validation.pdf.gz | 761.4 KB | Display | |
Data in XML | 1fnm_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 1fnm_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/1fnm ftp://data.pdbj.org/pub/pdb/validation_reports/fn/1fnm | 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: 76910.031 Da / Num. of mol.: 1 / Mutation: H573A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11C (NOVAGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P13551 |
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#2: Chemical | ChemComp-MG / |
#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: 2.43 Å3/Da / Density % sol: 49.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PEG 8000 (Fluka), guanosine 5'-diphophate, magnesium chloride , pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 0.935 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25 Å / Num. all: 18060 / Num. obs: 18060 / % possible obs: 94.8 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.41 / Num. unique all: 2011 / % possible all: 96.8 |
Reflection | *PLUS Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 96.8 % |
-Processing
Software |
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Refinement | Resolution: 2.8→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 3.6 % / Rfactor obs: 0.212 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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