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- PDB-1efm: STRUCTURE OF THE GDP DOMAIN OF EF-TU AND LOCATION OF THE AMINO AC... -

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Basic information

Entry
Database: PDB / ID: 1efm
TitleSTRUCTURE OF THE GDP DOMAIN OF EF-TU AND LOCATION OF THE AMINO ACIDS HOMOLOGOUS TO RAS ONCOGENE PROTEINS
ComponentsELONGATION FACTOR TU
KeywordsELONGATION FACTOR
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 ...Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu / Elongation factor Tu 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsJurnak, F.
Citation
Journal: Science / Year: 1985
Title: Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins.
Authors: Jurnak, F.
#1: Journal: J.Biol.Chem. / Year: 1980
Title: Biochemical and Structural Studies of the Tetragonal Crystalline Modification of the Escherichia Coli Elongation Factor TU
Authors: Jurnak, F. / McPherson, A. / Wang, A.H.J. / Rich, A.
#2: Journal: J.Mol.Biol. / Year: 1977
Title: Preliminary X-Ray Diffraction Data for Tetragonal Crystals of Trypsinized Escherichia Coli Elongation Factor
Authors: Jurnak, F. / Rich, A. / Miller, D.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Primary Structure of Elongation Factor TU from Escherichia Coli
Authors: Arai, K. / Clark, B.F.C. / Duffy, L. / Jones, M.D. / Kaziro, Y. / Laursen, R.A. / L'Italien, J. / Miller, D.L. / Nagarkatti, S. / Nakamura, S. / Nielsen, K.M. / Petersen, T.E. / Takahashi, K. / Wade, M.
History
DepositionMay 29, 1987Processing site: BNL
Revision 1.0Jul 16, 1987Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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

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Assembly

Deposited unit
A: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1193
Polymers41,6521
Non-polymers4682
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.609, 100.807, 162.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 41651.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02990, UniProt: P0CE48*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
Compound detailsTRYPSIN-MODIFIED EF-TU CONTAINS TWO MAJOR FRAGMENTS CONSISTING OF RESIDUES 1-44 AND 59-393. ...TRYPSIN-MODIFIED EF-TU CONTAINS TWO MAJOR FRAGMENTS CONSISTING OF RESIDUES 1-44 AND 59-393. RESIDUES 45-58 HAVE BEEN EXCISED. TO CLARIFY THIS RELATIONSHIP, THE PROTEIN IS REPRESENTED BY ONE SET OF SEQRES RECORDS WITH EXC IN PLACE OF RESIDUES 45-58.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.88 Å3/Da / Density % sol: 74.77 %
Crystal grow
*PLUS
Temperature: 4,8,14,20 and 22 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 185.215-217
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
119 mg/mlEF-Tu-GDP1droptrypsin-modified
250 mMTris-HCl1drop
310 mM1dropMgCl2
410 mM2-mercaptoethanol1drop
52 mMGDP1drop
63 %(w/v)PEG33501drop
730 %(w/v)PEG33501reservoir

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Processing

RefinementHighest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms158 0 29 0 187

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