tRNA wobble uridine modification / tRNA methylation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function
The biological assembly is a homodimer (obtained by superimposition of the full-length molecule (A) and the N-terminal domain (B)). Dimerisation via the N-terminal domain is essential for the formation of the THF-binding site.
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Components
#1: Protein
ProbabletRNAmodificationGTPasetrmE / TrmE GTP-binding protein
Mass: 54189.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TrmE / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 (TrmE-) / References: UniProt: Q9WYA4
#2: Protein
ProbabletRNAmodificationGTPasetrmE / TrmE GTP-binding protein
Mass: 16495.090 Da / Num. of mol.: 1 / Fragment: N-terminal domain (residues 1-118) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TrmE / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 (TrmE-) / References: UniProt: Q9WYA4
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.934 Å / Relative weight: 1
Reflection
Resolution: 2.3→19.7 Å / Num. all: 44838 / Num. obs: 44730 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 6 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.5
Reflection shell
Resolution: 2.3→2.4 Å / Redundancy: 6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.05 / Num. unique all: 5335 / % possible all: 99.7
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Processing
Software
Name
Classification
XDS
datascaling
XSCALE
datascaling
SHARP
phasing
CNS
refinement
XDS
datareduction
Refinement
Method to determine structure: SAD / Resolution: 2.3→19.7 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: THe authors are not sure about the position of the two SO4 ions with the high B-factors. From the density shape they would expect this type of Ion there due to the Ammonium Sulphate condition.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.252
2237
-
RANDOM
Rwork
0.226
-
-
-
all
0.227
44838
-
-
obs
0.227
44730
99.6 %
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Displacement parameters
Biso mean: 60.4 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-10.55 Å2
-1.34 Å2
0 Å2
2-
-
-10.55 Å2
0 Å2
3-
-
-
21.1 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.34 Å
0.3 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.32 Å
0.3 Å
Refinement step
Cycle: LAST / Resolution: 2.3→19.7 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4546
0
25
137
4708
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
x_bond_d
0.006
X-RAY DIFFRACTION
x_angle_deg
1.3
X-RAY DIFFRACTION
x_torsion_deg
22.3
X-RAY DIFFRACTION
x_torsion_impr_deg
0.88
+
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