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- PDB-1efu: ELONGATION FACTOR COMPLEX EF-TU/EF-TS FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1efu
TitleELONGATION FACTOR COMPLEX EF-TU/EF-TS FROM ESCHERICHIA COLI
Components
  • ELONGATION FACTOR TS
  • ELONGATION FACTOR TU
KeywordsCOMPLEX (TWO ELONGATION FACTORS) / ELONGATION FACTOR
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / guanyl-nucleotide exchange factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding ...guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / guanyl-nucleotide exchange factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / GTP Cyclohydrolase I; Chain A, domain 1 ...GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / GTP Cyclohydrolase I; Chain A, domain 1 / Tetrahydropterin Synthase; Chain A / Ubiquitin-associated (UBA) domain / 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 / UBA-like superfamily / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Helicase, Ruva Protein; domain 3 / 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 / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor Tu 1 / Elongation factor Ts / Elongation factor Tu 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsKawashima, T. / Berthet-Colominas, C. / Wulff, M. / Cusack, S. / Leberman, R.
Citation
Journal: Nature / Year: 1996
Title: The structure of the Escherichia coli EF-Tu.EF-Ts complex at 2.5 A resolution.
Authors: Kawashima, T. / Berthet-Colominas, C. / Wulff, M. / Cusack, S. / Leberman, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Interconversion of Crystals of the Escherichia Coli EF-TU.EF-Ts Complex between High-and Low-Diffraction Forms
Authors: Kawashima, T. / Berthet-Colominas, C. / Cusack, S. / Leberman, R.
History
DepositionJul 9, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

Downloads & links

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Assembly

Deposited unit
A: ELONGATION FACTOR TU
B: ELONGATION FACTOR TS
C: ELONGATION FACTOR TU
D: ELONGATION FACTOR TS


Theoretical massNumber of molelcules
Total (without water)145,1264
Polymers145,1264
Non-polymers00
Water21,3121183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-61 kcal/mol
Surface area53920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.533, 108.537, 194.550
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 TU / ELONGATION FACTOR FOR TRANSFER / HEAT UNSTABLE / EF-TU


Mass: 42230.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: N4830-1 / Plasmid: CPC40 / Gene (production host): TSF / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6N1, UniProt: P0CE48*PLUS
#2: Protein ELONGATION FACTOR TS / ELONGATION FACTOR FOR TRANSFER / HEAT STABLE / EF-TS


Mass: 30332.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: N4830-1
Description: THE CPC40 WITH THE TSF GENE INSERTED WAS USED TO TRANSFORM N4830-1. THIS LEAD TO THE COPURIFICATION OF EF-TU AND EF-TS.
Plasmid: CPC40 / Gene (production host): TSF / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6P1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.7 / Details: pH 7.7
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 19-20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 %PEG60001reservoir
220 %PEG4001reservoir
3100 mM1reservoirKNO3
464.4 mMTris-acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.883
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 13, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.883 Å / Relative weight: 1
ReflectionResolution: 2.48→44.28 Å / Num. obs: 51804 / % possible obs: 98.2 % / Observed criterion σ(I): 4 / Redundancy: 3.8 % / Biso Wilson estimate: 47.66 Å2 / Rsym value: 0.043 / Net I/σ(I): 13.8
Reflection shellResolution: 2.48→2.55 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.151 / % possible all: 80.3

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMV. 5.3data reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.283 -5 %
Rwork0.175 --
obs0.175 52652 -
Displacement parametersBiso mean: 37.3 Å2
Refine analyzeLuzzati sigma a obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9840 0 0 1183 11023
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.5→2.61 Å
RfactorNum. reflection% reflection
Rfree0.3506 --
Rwork0.2762 6155 -
obs--99.2 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25

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