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- PDB-1elo: ELONGATION FACTOR G WITHOUT NUCLEOTIDE -

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Basic information

Entry
Database: PDB / ID: 1elo
TitleELONGATION FACTOR G WITHOUT NUCLEOTIDE
ComponentsELONGATION FACTOR GEF-G
KeywordsELONGATION FACTOR / RIBOSOMAL TRANSLOCASE / GTP BINDING PROTEIN / HYDROLASE
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV ...Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / 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 / Translation factors / EF-G domain III/V-like / Ribosomal Protein S5; domain 2 / 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. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsAevarsson, A. / Brazhnikov, E. / Garber, M. / Zheltonosova, J. / Chirgadze, Yu. / Al-Karadaghi, S. / Svensson, L.A. / Liljas, A.
Citation
Journal: EMBO J / Year: 1994
Title: Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus.
Authors: A AEvarsson / E Brazhnikov / M Garber / J Zheltonosova / Y Chirgadze / S al-Karadaghi / L A Svensson / A Liljas /
Abstract: The crystal structure of Thermus thermophilus elongation factor G without guanine nucleotide was determined to 2.85 A. This GTPase has five domains with overall dimensions of 50 x 60 x 118 A. The GTP ...The crystal structure of Thermus thermophilus elongation factor G without guanine nucleotide was determined to 2.85 A. This GTPase has five domains with overall dimensions of 50 x 60 x 118 A. The GTP binding domain has a core common to other GTPases with a unique subdomain which probably functions as an intrinsic nucleotide exchange factor. Domains I and II are homologous to elongation factor Tu and their arrangement, both with and without GDP, is more similar to elongation factor Tu in complex with a GTP analogue than with GDP. Domains III and V show structural similarities to ribosomal proteins. Domain IV protrudes from the main body of the protein and has an extraordinary topology with a left-handed cross-over connection between two parallel beta-strands.
#1: Journal: To be Published
Title: The Structure of Elongation Factor G in Complex with Gdp: Conformational Flexibility and Nucleotide Exchange
Authors: Al-Karadaghi, S. / Aevarsson, A. / Zheltonosova, J. / Garber, M. / Liljas, A.
#2: Journal: J.Mol.Evol. / Year: 1995
Title: Structure-Based Sequence Alignment of Elongation Factors TU and G with Related Gtpases Involved in Translation
Authors: Aevarsson, A.
#3: Journal: Curr.Opin.Struct.Biol. / Year: 1995
Title: Ribosomal Proteins and Elongation Factors
Authors: Liljas, A. / Garber, M.
#4: 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
DepositionMar 13, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELONGATION FACTOR G


Theoretical massNumber of molelcules
Total (without water)76,9771
Polymers76,9771
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.600, 106.000, 116.400
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 / EF-G / TRANSLOCASE


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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Casale, E., (1991) J. Mol. Biol., 222, 447. / PH range low: 7 / PH range high: 4.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.05 Msuccinate1reservoir
33.3 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection% possible obs: 87 % / Observed criterion σ(I): 3

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 0
Details: PLEASE NOTE THAT THE "EFFECTOR" REGION (RESIDUES 40 - 67) IS INVISIBLE AND DOMAIN III IS DISORDERED AND POORLY VISIBLE IN MAPS. ASSIGNMENT OF SEQUENCE AND THE MODEL OF DOMAIN III IS VERY ...Details: PLEASE NOTE THAT THE "EFFECTOR" REGION (RESIDUES 40 - 67) IS INVISIBLE AND DOMAIN III IS DISORDERED AND POORLY VISIBLE IN MAPS. ASSIGNMENT OF SEQUENCE AND THE MODEL OF DOMAIN III IS VERY UNCERTAIN (RESIDUES 400 - 475). TEMPERATURE FACTORS HAVE NOT BEEN REFINED AND SOLVENT MOLECULES HAVE NOT BEEN INCLUDED.
RfactorNum. reflection% reflection
Rfree0.32 -10 %
Rwork0.23 --
obs0.23 18281 -
Displacement parametersBiso mean: 22.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4957 0 0 0 4957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.29

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