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- PDB-5mi3: Structure of phosphorylated translation elongation factor EF-Tu f... -

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Basic information

Entry
Database: PDB / ID: 5mi3
TitleStructure of phosphorylated translation elongation factor EF-Tu from E. coli
ComponentsElongation factor Tu 1EF-Tu
KeywordsHYDROLASE / translation elongation / EF-Tu / phosphorylation / nucleotide binding / protein dynamics / conformational cycle / toxin-antitoxin / TOXIN
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTalavera, A. / Hendrix, J. / Versees, W. / De Gieter, S. / Castro-Roa, D. / Jurenas, D. / Van Nerom, K. / Vandenberk, N. / Barth, A. / De Greve, H. ...Talavera, A. / Hendrix, J. / Versees, W. / De Gieter, S. / Castro-Roa, D. / Jurenas, D. / Van Nerom, K. / Vandenberk, N. / Barth, A. / De Greve, H. / Hofkens, J. / Zenkin, N. / Loris, R. / Garcia-Pino, A.
Funding support Belgium, 1items
OrganizationGrant numberCountry
FNRSMIS F.4505.16 Belgium
CitationJournal: Sci Adv / Year: 2018
Title: Phosphorylation decelerates conformational dynamics in bacterial translation elongation factors.
Authors: Talavera, A. / Hendrix, J. / Versees, W. / Jurenas, D. / Van Nerom, K. / Vandenberk, N. / Singh, R.K. / Konijnenberg, A. / De Gieter, S. / Castro-Roa, D. / Barth, A. / De Greve, H. / Sobott, ...Authors: Talavera, A. / Hendrix, J. / Versees, W. / Jurenas, D. / Van Nerom, K. / Vandenberk, N. / Singh, R.K. / Konijnenberg, A. / De Gieter, S. / Castro-Roa, D. / Barth, A. / De Greve, H. / Sobott, F. / Hofkens, J. / Zenkin, N. / Loris, R. / Garcia-Pino, A.
History
DepositionNov 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_name_com / entity_src_gen / reflns / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _reflns.pdbx_Rmerge_I_obs / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu 1
B: Elongation factor Tu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7226
Polymers88,7872
Non-polymers9354
Water4,396244
1
A: Elongation factor Tu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8613
Polymers44,3931
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elongation factor Tu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8613
Polymers44,3931
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.200, 244.400, 61.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Elongation factor Tu 1 / EF-Tu / EF-Tu 1 / Bacteriophage Q beta RNA-directed RNA polymerase subunit III / P-43


Mass: 44393.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Thr 391 is phosphorylated
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: tufA, b3339, JW3301 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CE47, UniProt: A8A5E6*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.: 244 / 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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaCl, 0.1 M MES and 10 % PEG4000. / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.8 Å / Num. obs: 25588 / % possible obs: 97.1 % / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.134 / Net I/σ(I): 19.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFC

1efc


Resolution: 2.8→45.771 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1984 1278 5 %
Rwork0.1533 --
obs0.1556 25541 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5828 0 58 244 6130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086021
X-RAY DIFFRACTIONf_angle_d1.0278193
X-RAY DIFFRACTIONf_dihedral_angle_d18.9963587
X-RAY DIFFRACTIONf_chiral_restr0.061946
X-RAY DIFFRACTIONf_plane_restr0.0071062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.9120.30211270.21822409X-RAY DIFFRACTION89
2.912-3.04450.27521280.20092438X-RAY DIFFRACTION90
3.0445-3.2050.22141380.17832614X-RAY DIFFRACTION96
3.205-3.40580.21121460.17562769X-RAY DIFFRACTION100
3.4058-3.66860.24251440.15982725X-RAY DIFFRACTION100
3.6686-4.03760.1811460.15142774X-RAY DIFFRACTION100
4.0376-4.62140.14581450.12352764X-RAY DIFFRACTION100
4.6214-5.82060.18181490.12542812X-RAY DIFFRACTION100
5.8206-45.77670.17521550.14232958X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.36140.1378-0.26893.145-0.18053.01450.08460.0017-0.0308-0.03660.003-0.03470.2855-0.0073-0.06660.07820.0192-0.01990.17890.00180.1121-17.752740.61254.9072
21.79940.2447-0.2631.2623-0.24631.7110.01650.0823-0.09510.0032-0.03670.08660.0494-0.26730.01720.0889-0.0107-0.01910.22450.0060.1849-44.970452.0584-7.2327
31.85540.2805-0.19541.8256-0.41142.3770.0235-0.026-0.11890.1870.0141-0.02490.61310.04-0.03720.66650.0072-0.0420.18340.01740.1921-22.298219.4925-29.3898
46.058-2.9949-3.85542.11952.07092.97930.3280.6989-0.0495-0.4616-0.3980.1812-0.1562-0.73270.04120.3737-0.070.00550.4733-0.04080.3062-54.121634.911-22.6839
51.4588-1.007-0.11173.08530.07081.1820.18760.2971-0.2987-0.5976-0.4370.55110.479-0.52380.20060.447-0.1136-0.02160.6341-0.10160.3623-57.545931.0996-21.9112
63.2284-0.61010.58452.1388-0.7412.37420.0395-0.6628-0.55060.6316-0.05340.3520.3289-0.15380.00590.9516-0.13950.14250.53960.07160.4928-44.023914.1428-9.6406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 199 )
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 394 )
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 199 )
4X-RAY DIFFRACTION4chain 'B' and (resid 200 through 231 )
5X-RAY DIFFRACTION5chain 'B' and (resid 232 through 311 )
6X-RAY DIFFRACTION6chain 'B' and (resid 312 through 394 )

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