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- PDB-5mi9: Structure of the phosphomimetic mutant of the elongation factor E... -

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Basic information

Entry
Database: PDB / ID: 5mi9
TitleStructure of the phosphomimetic mutant of the elongation factor EF-Tu T62E
ComponentsElongation factor Tu 1EF-Tu
KeywordsHYDROLASE / phosphomimetic protein / nucleotide binding / conformational cycle / protein dynamics / translation elongation / toxin-antitoxin
Function / homology
Function and homology information


guanosine tetraphosphate binding / 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 1
Similarity search - Component
Biological speciesEscherichia coli O9:H4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)89,6506
Polymers88,7152
Non-polymers9354
Water19811
1
A: Elongation factor Tu 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8253
Polymers44,3581
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)44,8253
Polymers44,3581
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.120, 62.100, 65.470
Angle α, β, γ (deg.)109.25, 106.00, 88.15
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Elongation factor Tu 1 / EF-Tu / EF-Tu 1


Mass: 44357.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O9:H4 (strain HS) (bacteria)
Strain: HS / Gene: tuf1, EcHS_A3535 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A8A5E6
#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.: 11 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M MgCl2, 0.1 M HEPES and 10 % PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.29→51.04 Å / Num. obs: 12489 / % possible obs: 98 % / Redundancy: 1.8 % / Biso Wilson estimate: 75 Å2 / Rrim(I) all: 0.147 / Net I/σ(I): 6.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→51.04 Å / Cor.coef. Fo:Fc: 0.8972 / Cor.coef. Fo:Fc free: 0.8911 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.52
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 614 5.01 %RANDOM
Rwork0.2257 ---
obs0.2271 12267 98.28 %-
Displacement parametersBiso mean: 108.45 Å2
Baniso -1Baniso -2Baniso -3
1--6.8333 Å2-2.7853 Å2-18.6266 Å2
2--3.4772 Å24.7705 Å2
3---3.3562 Å2
Refine analyzeLuzzati coordinate error obs: 0.8 Å
Refinement stepCycle: 1 / Resolution: 3.3→51.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 58 11 5245
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115343HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.287350HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1569SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes882HARMONIC5
X-RAY DIFFRACTIONt_it5343HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion20.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion783SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5699SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.62 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3064 146 5 %
Rwork0.2324 2773 -
all0.2361 2919 -
obs--98.28 %
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)
11.8234-0.0323-0.4562.17481.0950.2509-0.1269-0.01230.1306-0.26080.1840.11360.1994-0.2702-0.05710.0148-0.0598-0.13350.177-0.0612-0.2721-45.8036-15.9084-2.2833
21.5930.48820.7982.50232.09232.2154-0.02380.05710.0791-0.0485-0.0941-0.12380.15040.21750.1179-0.0608-0.130.11930.0612-0.1221-0.1892-26.0136-33.417616.4396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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