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- PDB-1tui: INTACT ELONGATION FACTOR TU IN COMPLEX WITH GDP -

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Basic information

Entry
Database: PDB / ID: 1tui
TitleINTACT ELONGATION FACTOR TU IN COMPLEX WITH GDP
ComponentsELONGATION FACTOR TUEF-Tu
KeywordsELONGATION FACTOR / PROTEIN BIOSYNTHESIS / GTP-BINDING
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / 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, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / 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 / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsPolekhina, G. / Thirup, S. / Kjeldgaard, M. / Nissen, P. / Lippmann, C. / Nyborg, J.
Citation
Journal: Structure / Year: 1996
Title: Helix unwinding in the effector region of elongation factor EF-Tu-GDP.
Authors: Polekhina, G. / Thirup, S. / Kjeldgaard, M. / Nissen, P. / Lippmann, C. / Nyborg, J.
#1: Journal: Science / Year: 1995
Title: Crystal Structure of the Ternary Complex of Phe-tRNAphe, EF-TU, and a GTP Analog
Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Polekhina, G. / Reshetnikova, L. / Clark, B.F. / Nyborg, J.
#2: Journal: Structure / Year: 1993
Title: The Crystal Structure of Elongation Factor EF-TU from Thermus Aquaticus in the GTP Conformation
Authors: Kjeldgaard, M. / Nissen, P. / Thirup, S. / Nyborg, J.
#3: Journal: Nature / Year: 1993
Title: Crystal Structure of Active Elongation Factor TU Reveals Major Domain Rearrangements
Authors: Berchtold, H. / Reshetnikova, L. / Reiser, C.O. / Schirmer, N.K. / Sprinzl, M. / Hilgenfeld, R.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Refined Structure of Elongation Factor EF-TU from Escherichia Coli
Authors: Kjeldgaard, M. / Nyborg, J.
History
DepositionMay 23, 1996Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)135,6319
Polymers134,2293
Non-polymers1,4036
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.900, 175.900, 223.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein ELONGATION FACTOR TU / EF-Tu


Mass: 44742.980 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / Strain: YT-1 / References: UniProt: Q01698
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.95 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlEF-Tu-GDP1drop
250 mMTris-HCl1drop
310 mM1dropMgCl2
410 mMbeta-mercaptoethanol1drop
50.1 mM1dropNaN3
610 mMGDP1drop
710 mMphenyl-methyl-sulphonylfluoride1drop
825 %ammonium sulfate1drop
950 mMTris-HCl1reservoir
1035 %ammonium sulfate1reservoir
110.8-1.0 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
Reflection% possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.067
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Num. obs: 56660
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 99.9 % / Num. unique obs: 5586 / Rmerge(I) obs: 0.434

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
RefinementResolution: 2.7→20 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.3 -
Rwork0.235 -
obs-54031
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9240 0 87 95 9422
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.235 / Rfactor Rfree: 0.306
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_dihedral_angle_deg20.2

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