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- PDB-3b0v: tRNA-dihydrouridine synthase from Thermus thermophilus in complex... -

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Basic information

Entry
Database: PDB / ID: 3b0v
TitletRNA-dihydrouridine synthase from Thermus thermophilus in complex with tRNA
Components
  • tRNA
  • tRNA-dihydrouridine synthase
KeywordsOXIDOREDUCTASE/RNA / Tim barrel / OXIDOREDUCTASE-RNA complex
Function / homology
Function and homology information


tRNA-dihydrouridine20a synthase activity / tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / FMN binding / flavin adenine dinucleotide binding / tRNA binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1460 / tRNA-dihydrouridine(20/20a) synthase / tRNA-dihydrouridine synthase / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Aldolase class I / Aldolase-type TIM barrel ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1460 / tRNA-dihydrouridine(20/20a) synthase / tRNA-dihydrouridine synthase / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / RNA / RNA (> 10) / tRNA-dihydrouridine(20/20a) synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.51 Å
AuthorsYu, F. / Tanaka, Y. / Yamashita, K. / Nakamura, A. / Yao, M. / Tanaka, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Molecular basis of dihydrouridine formation on tRNA
Authors: Yu, F. / Tanaka, Y. / Yamashita, K. / Suzuki, T. / Nakamura, A. / Hirano, N. / Suzuki, T. / Yao, M. / Tanaka, I.
History
DepositionJun 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA
B: tRNA
C: tRNA-dihydrouridine synthase
D: tRNA-dihydrouridine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7266
Polymers131,8134
Non-polymers9132
Water00
1
A: tRNA
C: tRNA-dihydrouridine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3633
Polymers65,9072
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-26 kcal/mol
Surface area23810 Å2
MethodPISA
2
B: tRNA
D: tRNA-dihydrouridine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3633
Polymers65,9072
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-28 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.890, 118.890, 319.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain tRNA


Mass: 24486.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: GenBank: AP008226
#2: Protein tRNA-dihydrouridine synthase


Mass: 41420.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0016 / Plasmid: CDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SMC7
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P

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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: 4.28 Å3/Da / Density % sol: 71.28 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Tris-HCl, ammonium sulfate, glycerol, pH 7-8, vapor diffusion, sitting drop, temperature 293K
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97881 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97881 Å / Relative weight: 1
ReflectionResolution: 3.51→48.605 Å / Num. all: 29454 / Num. obs: 29454 / % possible obs: 99.5 % / Redundancy: 13.2 % / Rsym value: 0.116 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.51-3.711.80.5550.5314.64793540770.1580.5550.5314.697.1
3.7-3.9313.20.3460.3336.85296640120.0950.3460.3336.899.9
3.93-4.213.50.2470.2389.65084037680.0670.2470.2389.6100
4.2-4.5313.70.1630.15714.34850735310.0440.1630.15714.3100
4.53-4.9713.90.120.11618.84567232780.0320.120.11618.8100
4.97-5.55140.1080.10420.64156729660.0290.1080.10420.6100
5.55-6.4113.80.1020.09823.73650626540.0270.1020.09823.7100
6.41-7.8513.20.0770.07430.73021722840.0210.0770.07430.7100
7.85-11.1112.80.0550.05343.62322618080.0150.0550.05343.6100
11.11-48.6059.80.0650.06134.21053310760.0190.0650.06134.298.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
CNS1.3refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.51→48.6 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 193421 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.32 2326 7.9 %RANDOM
Rwork0.3 ---
obs-29334 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 105.155 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 284.43 Å2 / Biso mean: 148.8284 Å2 / Biso min: 73.76 Å2
Baniso -1Baniso -2Baniso -3
1-31.45 Å20 Å20 Å2
2--31.45 Å20 Å2
3----62.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å0.87 Å
Refinement stepCycle: LAST / Resolution: 3.51→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 3122 62 0 8204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d2.88
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.82
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 350 7.9 %
Rwork0.386 4072 -
all-4422 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6FMN.paramFMN.top
X-RAY DIFFRACTION7H2U.paramH2U.top

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