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- PDB-4fn5: ELONGATION FACTOR G 1 (PSEUDOMONAS AERUGINOSA) IN COMPLEX WITH Ar... -

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Basic information

Entry
Database: PDB / ID: 4fn5
TitleELONGATION FACTOR G 1 (PSEUDOMONAS AERUGINOSA) IN COMPLEX WITH Argyrin B
Components
  • Argyrin B
  • Elongation factor G 1EF-G
KeywordsTRANSLATION/ANTIBIOTIC / Elongation Factor / TRANSLATION / TRANSLATION-ANTIBIOTIC complex
Function / homology
Function and homology information


ribosome disassembly / translation elongation factor activity / GTPase activity / GTP binding / cytosol
Similarity search - Function
Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV ...Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Translation factors / EF-G domain III/V-like / Ribosomal Protein S5; domain 2 / 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 / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Elongation factor G 1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Actinoplanes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKirby, C.A. / Palestrant, D.
CitationJournal: Plos One / Year: 2012
Title: Identification of elongation factor g as the conserved cellular target of argyrin B.
Authors: Nyfeler, B. / Hoepfner, D. / Palestrant, D. / Kirby, C.A. / Whitehead, L. / Yu, R. / Deng, G. / Caughlan, R.E. / Woods, A.L. / Jones, A.K. / Barnes, S.W. / Walker, J.R. / Gaulis, S. / Hauy, ...Authors: Nyfeler, B. / Hoepfner, D. / Palestrant, D. / Kirby, C.A. / Whitehead, L. / Yu, R. / Deng, G. / Caughlan, R.E. / Woods, A.L. / Jones, A.K. / Barnes, S.W. / Walker, J.R. / Gaulis, S. / Hauy, E. / Brachmann, S.M. / Krastel, P. / Studer, C. / Riedl, R. / Estoppey, D. / Aust, T. / Movva, N.R. / Wang, Z. / Salcius, M. / Michaud, G.A. / McAllister, G. / Murphy, L.O. / Tallarico, J.A. / Wilson, C.J. / Dean, C.R.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor G 1
B: Argyrin B


Theoretical massNumber of molelcules
Total (without water)79,0362
Polymers79,0362
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-7 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.780, 88.100, 74.320
Angle α, β, γ (deg.)90.00, 107.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 78160.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fusA, fusA1, PA4266 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWD2
#2: Protein/peptide Argyrin B


Mass: 874.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Actinoplanes sp. (bacteria) / Strain: 86317
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PROTEIN SOLUTION WAS INCUBATED WITH LIGAND FOR 1 HOUR. EQUAL VOLUMES OF RESERVOIR SOLUTION AND PROTEIN SOLUTION WERE MIXED. Reservoir Solution: 100MM TRIS HCL PH 7.5, 18% PEG3350, 0.2M ...Details: PROTEIN SOLUTION WAS INCUBATED WITH LIGAND FOR 1 HOUR. EQUAL VOLUMES OF RESERVOIR SOLUTION AND PROTEIN SOLUTION WERE MIXED. Reservoir Solution: 100MM TRIS HCL PH 7.5, 18% PEG3350, 0.2M Sodium NITRATE. PROTEIN SOLUTION: 50MM TRIS HCL PH7.5, 150MM NACL, 1MM TCEP , VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→71 Å / Num. obs: 16883 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 84.47 Å2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
APS17-IDdata collection
PHASERphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→55.39 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.8248 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 857 5.06 %RANDOM
Rwork0.2017 ---
obs0.2068 -98.13 %-
Displacement parametersBiso mean: 77.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.0185 Å20 Å229.5681 Å2
2---9.5165 Å20 Å2
3---11.535 Å2
Refine analyzeLuzzati coordinate error obs: 0.419 Å
Refinement stepCycle: LAST / Resolution: 2.9→55.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5237 0 0 16 5253
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015322HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.37180HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1905SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes146HARMONIC2
X-RAY DIFFRACTIONt_gen_planes764HARMONIC5
X-RAY DIFFRACTIONt_it5322HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion22.09
X-RAY DIFFRACTIONt_chiral_improper_torsion692SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6036SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3365 146 5.38 %
Rwork0.2436 2569 -
all0.2483 2715 -
obs--98.13 %

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