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- PDB-1tfe: DIMERIZATION DOMAIN OF EF-TS FROM T. THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1tfe
TitleDIMERIZATION DOMAIN OF EF-TS FROM T. THERMOPHILUS
ComponentsELONGATION FACTOR TS
KeywordsELONGATION FACTOR
Function / homology
Function and homology information


translation elongation factor activity / 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 / UBA-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor Ts
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsJiang, Y. / Nock, S. / Nesper, M. / Sprinzl, M. / Sigler, P.B.
CitationJournal: Biochemistry / Year: 1996
Title: Structure and importance of the dimerization domain in elongation factor Ts from Thermus thermophilus.
Authors: Jiang, Y. / Nock, S. / Nesper, M. / Sprinzl, M. / Sigler, P.B.
History
DepositionApr 16, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELONGATION FACTOR TS


Theoretical massNumber of molelcules
Total (without water)16,7281
Polymers16,7281
Non-polymers00
Water4,666259
1
A: ELONGATION FACTOR TS

A: ELONGATION FACTOR TS


Theoretical massNumber of molelcules
Total (without water)33,4572
Polymers33,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)60.100, 60.100, 94.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ELONGATION FACTOR TS


Mass: 16728.453 Da / Num. of mol.: 1 / Fragment: EF-TS DIMERIZATION DOMAIN, RESIDUES 55 - 196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Cell line: BL21 / Gene: TSF / Plasmid: PET28C / Species (production host): Escherichia coli / Gene (production host): TSF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P43895
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.94 Å3/Da / Density % sol: 60 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
255 mMTris-HCl1drop
35 %PEG30001drop
420 mM1dropCaCl2
510 %PEG30001reservoir
640 mM1reservoirCaCl2
7100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 24914 / % possible obs: 93.5 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.6→50 Å / % possible all: 85.9
Reflection shell
*PLUS
% possible obs: 88.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
DPHASEmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
DPHASEphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.285 -10 %
Rwork0.207 --
obs0.207 19706 -
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1149 0 0 259 1408
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.476
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.49
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.467
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 21390 / Rfactor all: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.49
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.467

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