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- PDB-3g5s: Crystal structure of Thermus thermophilus TrmFO in complex with g... -

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Basic information

Entry
Database: PDB / ID: 3g5s
TitleCrystal structure of Thermus thermophilus TrmFO in complex with glutathione
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 / GLUTATHIONE / Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 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 1.2Dec 14, 2011Group: Non-polymer description

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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)51,0059
Polymers49,5781
Non-polymers1,4288
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.257, 92.226, 104.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 49577.605 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, 649 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-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 13% PEG 3350, 0.1M magnesium chloride, 0.05M Tris-HCl (pH 8.5), 10mM reduced-glutathione, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.9
SYNCHROTRONPhoton Factory AR-NW12A20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 7, 2008
ADSC QUANTUM 2102CCDMay 30, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97931
ReflectionResolution: 1.05→43.85 Å / Num. obs: 209948 / Biso Wilson estimate: 11.37 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: SAD / Resolution: 1.05→43.811 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.924 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 14.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1784 19458 5.04 %RANDOM
Rwork0.1622 ---
obs0.163 209897 91.83 %-
all-217119 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.854 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 51.15 Å2 / Biso mean: 18.669 Å2 / Biso min: 8.13 Å2
Baniso -1Baniso -2Baniso -3
1-2.705 Å2-0 Å2-0 Å2
2---4.357 Å20 Å2
3----1.586 Å2
Refinement stepCycle: LAST / Resolution: 1.05→43.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 94 641 4022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063515
X-RAY DIFFRACTIONf_angle_d1.1794774
X-RAY DIFFRACTIONf_chiral_restr0.082506
X-RAY DIFFRACTIONf_plane_restr0.014624
X-RAY DIFFRACTIONf_dihedral_angle_d17.1891331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.05-1.06190.24894840.2489855365
1.0619-1.07440.24335190.2429961772
1.0744-1.08750.23455410.23031015276
1.0875-1.10130.22216170.21831046579
1.1013-1.11570.20795780.20541105383
1.1157-1.1310.20826180.19921140086
1.131-1.14720.19885140.18971180488
1.1472-1.16430.19736170.1821182089
1.1643-1.18250.19456630.17431214391
1.1825-1.20190.18946150.16861217391
1.2019-1.22260.16866110.16531228092
1.2226-1.24490.16786940.15851235193
1.2449-1.26880.17876650.15231250294
1.2688-1.29470.17136370.14471253094
1.2947-1.32290.15616370.14031262795
1.3229-1.35360.14917200.13131260395
1.3536-1.38750.14197210.13121264595
1.3875-1.4250.15966820.12491280496
1.425-1.46690.13257010.12571288297
1.4669-1.51430.13797150.12141285297
1.5143-1.56840.12756400.12251300498
1.5684-1.63120.14627000.12291300898
1.6312-1.70550.15027520.13051298098
1.7055-1.79540.15766200.13791317598
1.7954-1.90790.16236220.14891316898
1.9079-2.05520.17796890.15141320999
2.0552-2.2620.17747690.160813295100
2.262-2.58920.18597140.172613244100
2.5892-3.2620.18727150.183113313100
3.262-43.84950.19626880.171313316100

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