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- PDB-1xb2: Crystal Structure of Bos taurus mitochondrial Elongation Factor T... -

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Basic information

Entry
Database: PDB / ID: 1xb2
TitleCrystal Structure of Bos taurus mitochondrial Elongation Factor Tu/Ts Complex
Components
  • Elongation factor Ts, mitochondrial
  • Elongation factor Tu, mitochondrialEF-Tu
KeywordsTRANSLATION / Protein-protein complex
Function / homology
Function and homology information


regulation of mitochondrial translation / mitochondrial translational elongation / translational elongation / translation elongation factor activity / mitochondrial inner membrane / mitochondrial matrix / GTPase activity / GTP binding / mitochondrion / cytosol
Similarity search - Function
Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / Tetrahydropterin Synthase; Chain A / Ubiquitin-associated (UBA) domain ...Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / Tetrahydropterin Synthase; Chain A / Ubiquitin-associated (UBA) domain / 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 / UBA-like superfamily / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Helicase, Ruva Protein; domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor Ts, mitochondrial / Elongation factor Tu, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJeppesen, M.G. / Navratil, T. / Spremulli, L.L. / Nyborg, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of the Bovine Mitochondrial Elongation Factor Tu.Ts Complex
Authors: Jeppesen, M.G. / Navratil, T. / Spremulli, L.L. / Nyborg, J.
History
DepositionAug 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor Tu, mitochondrial
B: Elongation factor Ts, mitochondrial


Theoretical massNumber of molelcules
Total (without water)77,5082
Polymers77,5082
Non-polymers00
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-11 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.0, 149.3, 70.0
Angle α, β, γ (deg.)90.0, 125.2, 90.0
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological unit consists of one molecule each of EF-Tu and EF-Ts

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Components

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


Mass: 45658.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: TUFM / Plasmid: EK-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49410
#2: Protein Elongation factor Ts, mitochondrial / EF-Ts / EF-TsMt


Mass: 31849.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: TSFM / Plasmid: pET24c(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43896
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 14-18% PEG 8000, 100 mM Tris-HCl pH 7.6, 200 mM Na3Citrate-2H2O, 2 mM DTT and 1 mM NaN3 , VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9818, 0.9824, 0.9716
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2004 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98181
20.98241
30.97161
ReflectionResolution: 2.18→30 Å / Num. all: 39819 / Num. obs: 38985 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 %
Reflection shellResolution: 2.18→2.28 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / Cross valid method: Trroughout / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1547 -Random
Rwork0.218 ---
all0.219 39183 --
obs0.219 37636 98.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 0 322 5294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.2→2.22 Å
RfactorNum. reflection
Rfree0.261 33
Rwork0.292 -
obs-1181

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