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- PDB-1efg: THE CRYSTAL STRUCTURE OF ELONGATION FACTOR G COMPLEXED WITH GDP, ... -

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Basic information

Entry
Database: PDB / ID: 1efg
TitleTHE CRYSTAL STRUCTURE OF ELONGATION FACTOR G COMPLEXED WITH GDP, AT 2.7 ANGSTROMS RESOLUTION
Components(ELONGATION FACTOR G) x 3
KeywordsELONGATION FACTOR
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 / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus ...Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor G / Elongation factor G
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsCzworkowski, 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: Nucleic Acids Res. / Year: 1989
Title: Nucleotide Sequence of the Thermus Thermophilus Hb8 Gene Coding for Elongation Factor G
Authors: Yakhnin, A.V. / Vorozheykina, D.P. / Matvienko, N.I.
History
DepositionOct 17, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELONGATION FACTOR G
B: ELONGATION FACTOR G
C: ELONGATION FACTOR G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8894
Polymers82,4463
Non-polymers4431
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.269, 115.447, 106.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ELONGATION FACTOR G / Coordinate model: Cα atoms only


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
#2: Protein/peptide ELONGATION FACTOR G / Coordinate model: Cα atoms only


Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#3: Protein/peptide ELONGATION FACTOR G / Coordinate model: Cα atoms only


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 277 K / pH: 7.8 / Details: pH 7.8, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-20 %(w/v)PEG80001reservoir
220 mMTris-HCl1reservoir
32 mMdithiothreitol1reservoir
41 mMGDP1reservoir
51 mM1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 26380 / % possible obs: 97.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.7→10 Å / σ(F): 2
Details: AN OVERALL TEMPERATURE FACTOR HAS BEEN DETERMINED FOR EACH OF THE FIVE DOMAINS.
RfactorNum. reflection% reflection
Rfree0.396 --
Rwork0.267 --
obs0.267 25632 97.8 %
Displacement parametersBiso mean: 33.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms656 0 28 0 684
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.267 / Rfactor Rfree: 0.396 / Rfactor Rwork: 0.267
Solvent computation
*PLUS
Displacement parameters
*PLUS

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