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- PDB-1xzp: Structure of the GTP-binding protein TrmE from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1xzp
TitleStructure of the GTP-binding protein TrmE from Thermotoga maritima
Components(Probable tRNA modification GTPase trmE) x 2
KeywordsHYDROLASE / GTP-binding / THF-binding / tRNA-modification
Function / homology
Function and homology information


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
tRNA modification GTPase MnmE domain 2 / tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / Probable tRNA modification gtpase trme; domain 1 ...tRNA modification GTPase MnmE domain 2 / tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / Probable tRNA modification gtpase trme; domain 1 / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / Guanylate kinase-like domain / 50S ribosome-binding GTPase / GTP binding domain / Gyrase A; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsScrima, A. / Vetter, I.R. / Armengod, M.E. / Wittinghofer, A.
CitationJournal: Embo J. / Year: 2005
Title: The structure of the TrmE GTP-binding protein and its implications for tRNA modification
Authors: Scrima, A. / Vetter, I.R. / Armengod, M.E. / Wittinghofer, A.
History
DepositionNov 12, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable tRNA modification GTPase trmE
B: Probable tRNA modification GTPase trmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1657
Polymers70,6842
Non-polymers4805
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-94 kcal/mol
Surface area27470 Å2
MethodPISA
2
A: Probable tRNA modification GTPase trmE
B: Probable tRNA modification GTPase trmE
hetero molecules

A: Probable tRNA modification GTPase trmE
B: Probable tRNA modification GTPase trmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,32914
Polymers141,3694
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area10830 Å2
ΔGint-213 kcal/mol
Surface area52690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.855, 128.855, 107.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsThe 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 Probable tRNA modification GTPase trmE / 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 Probable tRNA modification GTPase trmE / 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 4.01 Å3/Da / Density % sol: 69.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulphate, mes, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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
NameClassification
XDSdata scaling
XSCALEdata scaling
SHARPphasing
CNSrefinement
XDSdata reduction
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2237 -RANDOM
Rwork0.226 ---
all0.227 44838 --
obs0.227 44730 99.6 %-
Displacement parametersBiso mean: 60.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.55 Å2-1.34 Å20 Å2
2---10.55 Å20 Å2
3---21.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 25 137 4708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg22.3
X-RAY DIFFRACTIONx_torsion_impr_deg0.88

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