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- PDB-1aip: EF-TU EF-TS COMPLEX FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1aip
TitleEF-TU EF-TS COMPLEX FROM THERMUS THERMOPHILUS
Components
  • ELONGATION FACTOR TS
  • ELONGATION FACTOR TUEF-Tu
KeywordsCOMPLEX OF TWO ELONGATION FACTORS / ELONGATION FACTOR / NUCLEOTIDE EXCHANGE / GTP-BINDING
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
GTP Cyclohydrolase I; Chain A, domain 1 - #20 / 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. / GTP Cyclohydrolase I; Chain A, domain 1 ...GTP Cyclohydrolase I; Chain A, domain 1 - #20 / 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. / GTP Cyclohydrolase I; Chain A, domain 1 / 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 / 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 / Helicase, Ruva Protein; 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 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor Ts / Elongation factor Tu-A
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsWang, Y. / Jiang, Y. / Meyering-Voss, M. / Sprinzl, M. / Sigler, P.B.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the EF-Tu.EF-Ts complex from Thermus thermophilus.
Authors: Wang, Y. / Jiang, Y. / Meyering-Voss, M. / Sprinzl, M. / Sigler, P.B.
History
DepositionApr 22, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELONGATION FACTOR TU
B: ELONGATION FACTOR TU
C: ELONGATION FACTOR TS
D: ELONGATION FACTOR TS
E: ELONGATION FACTOR TU
F: ELONGATION FACTOR TU
G: ELONGATION FACTOR TS
H: ELONGATION FACTOR TS


Theoretical massNumber of molelcules
Total (without water)268,7568
Polymers268,7568
Non-polymers00
Water27015
1
A: ELONGATION FACTOR TU
B: ELONGATION FACTOR TU
C: ELONGATION FACTOR TS
D: ELONGATION FACTOR TS


Theoretical massNumber of molelcules
Total (without water)134,3784
Polymers134,3784
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-58 kcal/mol
Surface area50520 Å2
MethodPISA
2
E: ELONGATION FACTOR TU
F: ELONGATION FACTOR TU
G: ELONGATION FACTOR TS
H: ELONGATION FACTOR TS


Theoretical massNumber of molelcules
Total (without water)134,3784
Polymers134,3784
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-55 kcal/mol
Surface area50900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.300, 127.500, 123.700
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999965, 0.000729, 0.008295), (0.00094, -0.999675, -0.025485), (0.008273, 0.025492, -0.999641)59.4207, 96.9949, 147.48061
2given(0.998645, -0.049045, -0.017367), (-0.049487, -0.998436, -0.025999), (-0.016065, 0.026824, -0.999511)62.54187, 95.65964, 146.46263

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Components

#1: Protein
ELONGATION FACTOR TU / EF-Tu / EF-TU


Mass: 44739.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P60338
#2: Protein
ELONGATION FACTOR TS / EF-TS


Mass: 22449.061 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P43895
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.53 Å3/Da / Density % sol: 66 %
Crystal growpH: 6.5
Details: 60 MM CACODYLATE, PH 6.5 70 MM AMMONIUM SULFATE 8% PEG 8000
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
25 mMTris-Cl1drop
35 mM 1dropKCl
41 mMEDTA1drop
560 mMcacodylate1drop
670 mMammonium sulfate1drop
78 %PEG80001drop
860 mMcacodylate1reservoir
970 mMammonium sulfate1reservoir
108 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 69409 / % possible obs: 92 % / Rsym value: 0.08 / Net I/σ(I): 15
Reflection shellResolution: 3.02→3.15 Å / Mean I/σ(I) obs: 3.96 / Rsym value: 0.372 / % possible all: 92.4
Reflection
*PLUS
Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 92.4 % / Rmerge(I) obs: 0.372

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 3→100 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 -5 %THIN SHELLS
Rwork0.216 ---
obs0.216 69409 92 %-
Refinement stepCycle: LAST / Resolution: 3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17564 0 0 15 17579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.29
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.15
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.66
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it6.121
X-RAY DIFFRACTIONx_mcangle_it9.331.5
X-RAY DIFFRACTIONx_scbond_it10.881.5
X-RAY DIFFRACTIONx_scangle_it15.22
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINEDX-RAY DIFFRACTION0.1250
22X-RAY DIFFRACTION0.046150
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3911 -3.05 %
Rwork0.3506 8322 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.15
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.66

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