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- PDB-2gj9: Structure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and Rb+ -

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Basic information

Entry
Database: PDB / ID: 2gj9
TitleStructure of the MnmE G-domain in complex with GDP*AlF4-, Mg2+ and Rb+
ComponentstRNA modification GTPase trmE
KeywordsHYDROLASE / G-domain dimer / alpha-beta-sandwich
Function / homology
Function and homology information


cytosolic tRNA wobble base thiouridylase complex / regulation of cytoplasmic translational fidelity / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / Hydrolases; Acting on acid anhydrides / tRNA methylation / response to pH / potassium ion binding / chaperone-mediated protein folding / GDP binding ...cytosolic tRNA wobble base thiouridylase complex / regulation of cytoplasmic translational fidelity / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / Hydrolases; Acting on acid anhydrides / tRNA methylation / response to pH / potassium ion binding / chaperone-mediated protein folding / GDP binding / GTPase activity / GTP binding / protein homodimerization activity / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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. / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase ...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. / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase / GTP binding domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / RUBIDIUM ION / tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsScrima, A. / Wittinghofer, A.
CitationJournal: Embo J. / Year: 2006
Title: Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element.
Authors: Scrima, A. / Wittinghofer, A.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: tRNA modification GTPase trmE
B: tRNA modification GTPase trmE
C: tRNA modification GTPase trmE
D: tRNA modification GTPase trmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,10420
Polymers74,4804
Non-polymers2,62416
Water25214
1
A: tRNA modification GTPase trmE
B: tRNA modification GTPase trmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,55210
Polymers37,2402
Non-polymers1,3128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: tRNA modification GTPase trmE
D: tRNA modification GTPase trmE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,55210
Polymers37,2402
Non-polymers1,3128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.240, 70.100, 90.210
Angle α, β, γ (deg.)90.00, 95.76, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit corresponds to a G-domain dimer.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
tRNA modification GTPase trmE / mnmE


Mass: 18620.121 Da / Num. of mol.: 4 / Fragment: G-domain (216-G384)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21DE3 / Gene: trmE, mnmE, thdF / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P25522

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Non-polymers , 5 types, 30 molecules

#2: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rb
#5: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16-19% PEG 3350, 100 mM MES pH 6.0, 200 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.815 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 48094 / % possible obs: 96.3 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.61
Reflection shell
Resolution (Å)Highest resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs
2-2.187.50.2283.41950711255
2.1-2.296.20.1894.82187910283
2.2-2.397.20.156180488457
2.3-2.498.20.1326.7158147347
2.4-2.598.30.1127.5133556190
2.5-398.40.0898.94328620044
3-498.50.05812.13428115856
4-597.40.04814.1121835630
5-698.50.04415.854352515
698.70.03418.357432687

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.864 / SU B: 5.499 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.299 2446 5.1 %RANDOM
Rwork0.25 ---
all0.252 47813 --
obs0.252 47813 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20.06 Å2
2--1.19 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4888 0 140 14 5042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0215088
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9956922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8935638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50523.519216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00415876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741552
X-RAY DIFFRACTIONr_chiral_restr0.1220.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023724
X-RAY DIFFRACTIONr_nbd_refined0.2320.22387
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2235
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.23
X-RAY DIFFRACTIONr_mcbond_it1.0581.53197
X-RAY DIFFRACTIONr_mcangle_it1.77225118
X-RAY DIFFRACTIONr_scbond_it2.81932049
X-RAY DIFFRACTIONr_scangle_it4.3994.51804
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 188 -
Rwork0.265 3225 -
obs-3413 97.15 %

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