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- PDB-1efc: INTACT ELONGATION FACTOR FROM E.COLI -

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Basic information

Entry
Database: PDB / ID: 1efc
TitleINTACT ELONGATION FACTOR FROM E.COLI
ComponentsPROTEIN (ELONGATION FACTOR)
KeywordsRNA BINDING PROTEIN / TRANSPORT AND PROTECTION PROTEIN
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 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsSong, H. / Parsons, M.R. / Rowsell, S. / Leonard, G. / Phillips, S.E.V.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution.
Authors: Song, H. / Parsons, M.R. / Rowsell, S. / Leonard, G. / Phillips, S.E.
#1: Journal: Structure / Year: 1996
Title: An Alpha to Beta Conformational Switch in EF-TU
Authors: Abel, K. / Yoder, M.D. / Hilgenfeld, R. / Jurnak, F.
#2: 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.
#3: Journal: Science / Year: 1995
Title: Crystal Structure of the Ternary Complex of Phe-tRNA, EF-TU and GTP Analogue
Authors: Nissen, P. / Kjeldgaard, M. / Thirup, S. / Polekhina, G. / Reshetnikova, L. / Clark, B.F.C. / Nyborg, J.
#4: Journal: Structure / Year: 1993
Title: The Crystal Structure of Elongation Factor EF-TU from T. Aquaticus in the GTP Conformation
Authors: Kjeldgaard, M. / Nissen, P. / Thirup, S. / Nyborg, J.
#5: Journal: J.Mol.Biol. / Year: 1992
Title: Refined Structure of Elongation Factor EF-TU from E. Coli
Authors: Kjeldgaard, M. / Nyborg, J.
History
DepositionNov 24, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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
A: PROTEIN (ELONGATION FACTOR)
B: PROTEIN (ELONGATION FACTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4146
Polymers86,4792
Non-polymers9354
Water8,035446
1
A: PROTEIN (ELONGATION FACTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7073
Polymers43,2391
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (ELONGATION FACTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7073
Polymers43,2391
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)243.120, 61.080, 66.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein PROTEIN (ELONGATION FACTOR) / EFTU


Mass: 43239.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6N1, UniProt: P0CE47*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.: 446 / Source method: isolated from a natural source / Formula: H2O
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 / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mMTris-HCl1drop
310 mM1dropMgCl2
41.2 Mammonium sulfate1drop
5100 mMTris-HCl1reservoir
610 mM1reservoirMgCl2
71.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97899,0.97916,0.91850
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1996 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.979161
30.91851
ReflectionResolution: 2.05→25 Å / Num. obs: 61876 / % possible obs: 90.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.274 / % possible all: 91.7
Reflection
*PLUS
Num. measured all: 217915
Reflection shell
*PLUS
% possible obs: 91.7 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→10 Å / Cross valid method: THROUGHOUT / ESU R: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2640 5 %RANDOM
Rwork0.203 ---
obs0.203 52808 90.5 %-
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 0 58 446 6444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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