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- PDB-4wfs: Crystal Structure of tRNA-dihydrouridine(20) synthase catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4wfs
TitleCrystal Structure of tRNA-dihydrouridine(20) synthase catalytic domain
ComponentstRNA-dihydrouridine(20) synthase [NAD(P)+]-like
KeywordsOXIDOREDUCTASE / RNA BINDING PROTEIN / tRNA PROCESSING / FLAVOPROTEIN
Function / homology
Function and homology information


tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / NADPH binding / antiviral innate immune response / PKR-mediated signaling / FMN binding ...tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / NADPH binding / antiviral innate immune response / PKR-mediated signaling / FMN binding / flavin adenine dinucleotide binding / double-stranded RNA binding / tRNA binding / endoplasmic reticulum / mitochondrion / cytoplasm / cytosol
Similarity search - Function
DUS2, double-stranded RNA binding domain / : / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain / Aldolase class I ...DUS2, double-stranded RNA binding domain / : / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsBou-Nader, C. / Pecqueur, L. / Kamah, A. / Bregeon, D. / Golinelli-Pimpaneau, B. / Guimaraes, B.G. / Fontecave, M. / Hamdane, D.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: An extended dsRBD is required for post-transcriptional modification in human tRNAs.
Authors: Bou-Nader, C. / Pecqueur, L. / Bregeon, D. / Kamah, A. / Guerineau, V. / Golinelli-Pimpaneau, B. / Guimaraes, B.G. / Fontecave, M. / Hamdane, D.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6817
Polymers36,8051
Non-polymers8766
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-64 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.570, 85.260, 144.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein tRNA-dihydrouridine(20) synthase [NAD(P)+]-like / Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine ...Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine synthase 2-like / hDUS2


Mass: 36805.359 Da / Num. of mol.: 1 / Fragment: DUS domain, UNP residues 14-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Plasmid: pET11d / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): STAR codon plus
References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Protein 8 mg/mL in Tris 25 mM pH 8.0 NaCl 150 mM Precipitant: Ammonium sulfate 2.2 M, isopropanol 2% v/v

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2012
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.68→43.64 Å / Num. obs: 12686 / % possible obs: 99.09 % / Redundancy: 7.2 % / Biso Wilson estimate: 54.9 Å2 / Net I/σ(I): 19.87
Reflection shellResolution: 2.68→2.77 Å / Redundancy: 7.12 % / Mean I/σ(I) obs: 2.69 / % possible all: 91.76

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B0P

3b0p


Resolution: 2.68→43.64 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9227 / SU R Cruickshank DPI: 0.484 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.494 / SU Rfree Blow DPI: 0.258 / SU Rfree Cruickshank DPI: 0.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 635 5.01 %RANDOM
Rwork0.1973 ---
obs0.1985 12684 99.44 %-
Displacement parametersBiso mean: 53.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.2361 Å20 Å20 Å2
2--6.3304 Å20 Å2
3----5.0943 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: 1 / Resolution: 2.68→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 52 28 2414
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012452HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073341HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1138SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes403HARMONIC5
X-RAY DIFFRACTIONt_it2452HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.55
X-RAY DIFFRACTIONt_other_torsion2.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion335SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3009SEMIHARMONIC4
LS refinement shellResolution: 2.68→2.94 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3103 147 5 %
Rwork0.2479 2794 -
all0.2509 2941 -
obs--99.44 %

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