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- PDB-1dg1: WHOLE, UNMODIFIED, EF-TU(ELONGATION FACTOR TU). -

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Basic information

Entry
Database: PDB / ID: 1dg1
TitleWHOLE, UNMODIFIED, EF-TU(ELONGATION FACTOR TU).
ComponentsELONGATION FACTOR TUEF-Tu
KeywordsRNA BINDING PROTEIN / ELONGATION FACTOR / TRNA BINDING / ALPHA BETA SHIFT / TS BINDING PROTEIN / GTPASE / GDP BINDING
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / 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, 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 1 / Elongation factor Tu 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAbel, K. / Yoder, M. / Hilgenfeld, R. / Jurnak, F.
CitationJournal: Structure / Year: 1996
Title: An alpha to beta conformational switch in EF-Tu.
Authors: Abel, K. / Yoder, M.D. / Hilgenfeld, R. / Jurnak, F.
History
DepositionNov 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: ELONGATION FACTOR TU
H: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6766
Polymers86,7412
Non-polymers9354
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.6, 104.6, 67.2
Angle α, β, γ (deg.)90.0, 97.02, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer, Tu with a GDP substrate bound.

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Components

#1: Protein ELONGATION FACTOR TU / EF-Tu / EF-TU


Mass: 43370.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CELL CYTOPLASM EXTRACT / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A6N1, UniProt: P0CE48*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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.: 2 / 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.: 193 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.75
Details: PEG 3350, ammonium citrate, ammonium acetate, pH 5.75, VAPOR DIFFUSION, temperature 298.0K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
210 mM1dropMgCl2
310 mM2-mercaptoethanol1drop
421.1 mg/mlprotein1drop
50.2 Mammonium sulfate1reservoir
60.1 Mammonium citrate1reservoir
724 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Mar 1, 1996 / Details: collimator
RadiationMonochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→63.123 Å / Num. all: 357998 / Num. obs: 28782 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.25 Å2 / Rsym value: 0.0613
Reflection
*PLUS
Num. measured all: 357998 / Rmerge(I) obs: 0.0678
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.68 Å / % possible obs: 91 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 2015 RANDOM
Rwork0.168 --
all0.172 269575 -
obs0.168 --
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5926 0 58 193 6177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.541
X-RAY DIFFRACTIONx_improper_angle_d1.282
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.282

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