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- PDB-3g5r: Crystal structure of Thermus thermophilus TrmFO in complex with t... -

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Basic information

Entry
Database: PDB / ID: 3g5r
TitleCrystal structure of Thermus thermophilus TrmFO in complex with tetrahydrofolate
ComponentsMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO
KeywordsTRANSFERASE / tRNA methyltransferase FAD folate / 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 / (6S)-5,6,7,8-TETRAHYDROFOLATE / Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.2Aug 24, 2011Group: Non-polymer description
Revision 1.3Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)50,56510
Polymers48,9211
Non-polymers1,6439
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.809, 97.023, 53.794
Angle α, β, γ (deg.)90.00, 101.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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]

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Non-polymers , 5 types, 387 molecules

#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-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG 8000, 0.2M calcium acetate, 0.1M Mes-NaOH (pH 6.5), 0.3mM tetrahydrofolic acid, 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: Nov 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→35.85 Å / Num. obs: 60724 / Biso Wilson estimate: 16.68 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: 1.6→35.841 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.907 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 16.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 3075 5.07 %RANDOM
Rwork0.1678 57635 --
obs0.1689 60710 97.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.507 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 67.11 Å2 / Biso mean: 21.886 Å2 / Biso min: 8.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.056 Å2-0 Å2-0.066 Å2
2---2.855 Å2-0 Å2
3---3.912 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 90 378 3708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043415
X-RAY DIFFRACTIONf_angle_d0.9434628
X-RAY DIFFRACTIONf_chiral_restr0.063495
X-RAY DIFFRACTIONf_plane_restr0.004599
X-RAY DIFFRACTIONf_dihedral_angle_d15.8391272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.599-1.6240.2241340.2308239289
1.624-1.65060.24531280.2248254595
1.6506-1.67910.22691340.2094256796
1.6791-1.70960.22091500.1997255996
1.7096-1.74250.21471380.1881260197
1.7425-1.77810.20151400.1777256297
1.7781-1.81670.20961450.1699262897
1.8167-1.8590.20651340.1724259798
1.859-1.90550.20081630.1677257198
1.9055-1.9570.20871180.1645266598
1.957-2.01460.1841090.1584267699
2.0146-2.07960.17531530.1474262899
2.0796-2.15390.16311440.1502267299
2.1539-2.24010.17431570.1488266299
2.2401-2.34210.19561580.1536263699
2.3421-2.46550.16881590.1576262899
2.4655-2.61990.2111380.1626264899
2.6199-2.82210.20511380.1714266499
2.8221-3.1060.19261360.16742711100
3.106-3.55510.14751330.15962688100
3.5551-4.47770.16041270.1438268799
4.4777-35.85030.18391390.1816264897

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