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- PDB-1etu: STRUCTURAL DETAILS OF THE BINDING OF GUANOSINE DIPHOSPHATE TO ELO... -

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Basic information

Entry
Database: PDB / ID: 1etu
TitleSTRUCTURAL DETAILS OF THE BINDING OF GUANOSINE DIPHOSPHATE TO ELONGATION FACTOR TU FROM E. COLI AS STUDIED BY X-RAY CRYSTALLOGRAPHY
ComponentsELONGATION FACTOR TU
KeywordsTRANSPORT AND PROTECTION PROTEIN
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 / magnesium ion binding / RNA binding ...guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / magnesium ion 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu 1 / Elongation factor Tu 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsClark, B.F.C. / Lacour, T.F.M. / Kjeldgaard, M. / Morikawa, K. / Nyborg, J. / Rubin, R. / Thirup, S.
Citation
Journal: EMBO J. / Year: 1985
Title: Structural details of the binding of guanosine diphosphate to elongation factor Tu from E. coli as studied by X-ray crystallography.
Authors: la Cour, T.F. / Nyborg, J. / Thirup, S. / Clark, B.F.
#1: Journal: Science / Year: 1985
Title: A Model for the Tertiary Structure of P21, the Product of the Ras Oncogene
Authors: Mccormick, F. / Clark, B.F.C. / Lacour, T.F.M. / Kjeldgaard, M. / Norskov-Lauritsen, L. / Nyborg, J.
#2: Journal: Gene Expression. The Translational Step and its Control
Year: 1984
Title: Structure of Bacterial Elongation Factor EF-TU and its Interaction with Aminoacyl-tRNA
Authors: Clark, B.F.C. / Lacour, T.F.M. / Nielsen, K.M. / Nyborg, J. / Petersen, H.U. / Siboska, G.E. / Wikman, F.P.
#3: Journal: FEBS Lett. / Year: 1981
Title: Structural Features of the Gdp Binding Site of Elongation Factor TU from Escherichia Coli as Determined by X-Ray Diffraction
Authors: Rubin, J.R. / Morikawa, K. / Nyborg, J. / Lacour, T.F.M. / Clark, B.F.C. / Miller, D.L.
#4: Journal: J.Mol.Biol. / Year: 1978
Title: High Resolution X-Ray Crystallographic Analysis of a Modified Form of the Elongation Factor TU(Colon) Guanosine Diphosphate Complex
Authors: Morikawa, K. / Lacour, T.F.M. / Nyborg, J. / Rasmussen, K.M. / Miller, D.L. / Clark, B.F.C.
History
DepositionJan 15, 1988Processing site: BNL
Revision 1.0Jul 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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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)43,6773
Polymers43,2091
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)98.200, 100.800, 160.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: SEE REMARK 5.

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Components

#1: Protein ELONGATION FACTOR TU


Mass: 43209.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A6N1, UniProt: P0CE47*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
Has protein modificationN
Sequence detailsEF-TU IS CODED FOR BY TWO DIFFERENT GENES. THE SEQUENCE STRUCTURE ANALYSIS CARRIED OUT ON THIS ...EF-TU IS CODED FOR BY TWO DIFFERENT GENES. THE SEQUENCE STRUCTURE ANALYSIS CARRIED OUT ON THIS MIXTURE SHOWS THAT THE C-TERMINAL RESIDUE OCCURS AS GLY/SER IN THE RATIO OF 3/1. THIS RESIDUE IS IDENTIFIED AS GLY ON THE *SEQRES* RECORDS BELOW.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.6 Å3/Da / Density % sol: 73.26 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion / Details: referred to J.Mol.Biol. 125.325-338
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-5 mg/mlEF-Tu:GDP1drop
210 mM1MgCl2
350 mMTris-HCl1
410 mMGDP1
55 %(w/v)PEG60001
610-12 %PEG1reservoir

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Processing

RefinementHighest resolution: 2.9 Å
Details: ATOMS WITH AN OCCUPANCY OF 0.0 ARE POORLY DEFINED IN THE DENSITY.
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 29 0 1395

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