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- PDB-3g5q: Crystal structure of Thermus thermophilus TrmFO -

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Basic information

Entry
Database: PDB / ID: 3g5q
TitleCrystal structure of Thermus thermophilus TrmFO
ComponentsMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO
KeywordsTRANSFERASE / tRNA methyltransferase FAD folate / Cytoplasm / FAD / Flavoprotein / Methyltransferase / tRNA processing
Function / homology
Function and homology information


methylenetetrahydrofolate-tRNA-(uracil54-C5)-methyltransferase [NAD(P)H-oxidizing] / tRNA (uracil(54)-C5)-methyltransferase activity, 5,10-methylenetetrahydrofolate-dependent / tRNA wobble uridine modification / tRNA methylation / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / MnmG-related, conserved site / Glucose inhibited division protein A family signature 2. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related / MnmG, N-terminal domain / Glucose inhibited division protein A / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsNishimasu, H. / Ishitani, R. / Hori, H. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase
Authors: Nishimasu, H. / Ishitani, R. / Yamashita, K. / Iwashita, C. / Hirata, A. / Hori, H. / Nureki, O.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8253
Polymers48,9211
Non-polymers9042
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.355, 75.370, 156.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

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Components

#1: Protein Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO / TrmFO / Folate-dependent tRNA (uracil-5-)-methyltransferase / Folate-dependent tRNA(M-5-U54)-methyltransferase


Mass: 48921.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: trmFO, TTHA1442 / Plasmid: pET-11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SID2, methylenetetrahydrofolate-tRNA-(uracil54-C5)-methyltransferase [NAD(P)H-oxidizing]
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 13% PEG 3350, 0.2M ammonium citrate tribasic, 0.1M Bicine-NaOH (pH 8.0), VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→42.477 Å / Num. obs: 23205 / Biso Wilson estimate: 21.85 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G5S

3g5s


Resolution: 2.102→42.477 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 16.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 1183 5.1 %RANDOM
Rwork0.1494 22000 --
obs0.152 23183 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.382 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 133.64 Å2 / Biso mean: 25.198 Å2 / Biso min: 8.21 Å2
Baniso -1Baniso -2Baniso -3
1-4.777 Å2-0 Å2-0 Å2
2---1.321 Å20 Å2
3----3.455 Å2
Refinement stepCycle: LAST / Resolution: 2.102→42.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 61 313 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073420
X-RAY DIFFRACTIONf_angle_d1.0964646
X-RAY DIFFRACTIONf_chiral_restr0.072497
X-RAY DIFFRACTIONf_plane_restr0.005606
X-RAY DIFFRACTIONf_dihedral_angle_d17.2111280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1018-2.19740.18251280.1319259893
2.1974-2.31330.22811410.147263394
2.3133-2.45820.21711450.1477265095
2.4582-2.64790.20171640.1507272997
2.6479-2.91440.19411410.1513276398
2.9144-3.33590.21581360.1514283199
3.3359-4.20230.18541560.1411285199
4.2023-42.48550.19491720.15722945100

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