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- PDB-8fr3: E. coli EF-Tu in complex with KKL-55 -

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Basic information

Entry
Database: PDB / ID: 8fr3
TitleE. coli EF-Tu in complex with KKL-55
ComponentsElongation factor TuEF-Tu
KeywordsTRANSLATION / EF-Tu / antibiotic
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 / 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 ...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 / 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. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / 3-chloro-N-(1-propyl-1H-tetrazol-5-yl)benzamide / Elongation factor Tu
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsNguyen, H.A. / Kuzmishin Nagy, A.B. / Dunham, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM121650 United States
CitationJournal: Mbio / Year: 2023
Title: Antibiotic that inhibits trans -translation blocks binding of EF-Tu to tmRNA but not to tRNA.
Authors: Marathe, N. / Nguyen, H.A. / Alumasa, J.N. / Kuzmishin Nagy, A.B. / Vazquez, M. / Dunham, C.M. / Keiler, K.C.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,0287
Polymers88,8272
Non-polymers1,2015
Water21612
1
A: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1474
Polymers44,4141
Non-polymers7333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8813
Polymers44,4141
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.385, 65.222, 70.559
Angle α, β, γ (deg.)107.670, 98.790, 107.080
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Elongation factor Tu / EF-Tu


Mass: 44413.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: tuf / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: E2QFJ4
#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: Chemical ChemComp-Y7C / 3-chloro-N-(1-propyl-1H-tetrazol-5-yl)benzamide


Mass: 265.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12ClN5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30-35% polyethylene glycol monomethyl ether 5,000 (PEG 5K MME), 0.2 M (NH4)2(SO4), 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.23→64.82 Å / Num. obs: 42498 / % possible obs: 93.98 % / Redundancy: 5.9 % / Biso Wilson estimate: 54.27 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1098 / Rpim(I) all: 0.04984 / Rrim(I) all: 0.1208 / Net I/σ(I): 9.79
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.8816 / Num. unique obs: 3782 / CC1/2: 0.777 / Rpim(I) all: 0.3918 / Rrim(I) all: 0.9666 / % possible all: 84.31

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6eze

6eze


Resolution: 2.23→64.82 Å / Cross valid method: THROUGHOUT / σ(F): 0.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 2038 4.799 %
Rwork0.2449 78820 -
obs0.2464 42465 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.9 Å2 / Biso mean: 62.25 Å2 / Biso min: 32.93 Å2
Refinement stepCycle: final / Resolution: 2.23→64.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5930 0 76 12 6018
Biso mean--65.42 55.08 -
Num. residues----770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.260.5367880.42241947203564
2.26-2.290.42251310.3882832296390
2.29-2.320.38371420.36832800294293
2.32-2.350.34771630.3772880304394
2.35-2.380.40411460.34572831297794
2.38-2.420.36051770.34152935311294
2.42-2.460.3361340.33062829296394
2.46-2.50.30551310.32082926305794
2.5-2.540.35661440.31642828297293
2.54-2.590.35951570.29232926308393
2.59-2.640.28791570.2992838299594
2.64-2.690.31641260.29732829295591
2.69-2.750.28991460.28312828297492
2.75-2.810.32461640.29372772293691
2.81-2.880.31421450.29642587273286
2.88-2.960.31051390.30942945308492
2.96-3.050.26141290.27882871300095
3.05-3.150.39691230.27722908303194
3.15-3.260.32961320.26482918305094
3.26-3.390.2491350.26642912304794
3.39-3.540.28471430.24362907305093
3.54-3.730.26111450.23912824296992
3.73-3.960.261380.21652792293091
3.96-4.270.21861410.21282615275685
4.27-4.70.24191340.19112981311595
4.7-5.380.22411860.19362851303795
5.38-6.770.28551550.23142862301794
6.78-64.820.23961180.20752846296491

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