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- PDB-6f00: Crystal Structure of human tRNA dihydrouridine synthase (20) dsRB... -

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Basic information

Entry
Database: PDB / ID: 6f00
TitleCrystal Structure of human tRNA dihydrouridine synthase (20) dsRBD E423A mutant
ComponentstRNA-dihydrouridine(20) synthase [NAD(P)+]-like
KeywordsRNA BINDING PROTEIN / double-stranded RNA binding domain
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 Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain ...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 Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Aldolase-type TIM barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.163 Å
AuthorsCharles, B.N. / Djemel, H.
CitationJournal: To Be Published
Title: Crystal Structure of human tRNA-dihydrouridine(20) synthase dsRBD E423A mutant
Authors: Charles, B.N. / Djemel, H.
History
DepositionNov 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,43318
Polymers41,0123
Non-polymers1,42115
Water3,369187
1
B: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0555
Polymers13,6711
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2357
Polymers13,6711
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1436
Polymers13,6711
Non-polymers4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.250, 52.210, 52.310
Angle α, β, γ (deg.)107.69, 107.92, 107.65
Int Tables number1
Space group name H-MP1

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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: 13670.661 Da / Num. of mol.: 3 / Mutation: E423A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6 M ammonium sulfate 100 mM sodium chloride 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.163→44.7 Å / Num. obs: 41560 / % possible obs: 95.99 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.0725 / Net I/σ(I): 7.58
Reflection shellResolution: 2.163→2.24 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6406 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2174 / CC1/2: 0.481 / % possible all: 92.16

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFT

4wft


Resolution: 2.163→44.7 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.19 / Phase error: 25.83
RfactorNum. reflection% reflection
Rfree0.2277 2093 5.04 %
Rwork0.1764 --
obs0.1791 41560 86.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.163→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 80 187 2554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132402
X-RAY DIFFRACTIONf_angle_d1.1023242
X-RAY DIFFRACTIONf_dihedral_angle_d18.0781474
X-RAY DIFFRACTIONf_chiral_restr0.114358
X-RAY DIFFRACTIONf_plane_restr0.007400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1628-2.21310.33771290.30192379X-RAY DIFFRACTION79
2.2131-2.26840.361420.28262607X-RAY DIFFRACTION85
2.2684-2.32980.28441310.28532525X-RAY DIFFRACTION87
2.3298-2.39830.32911410.26182627X-RAY DIFFRACTION84
2.3983-2.47570.31751400.24472677X-RAY DIFFRACTION84
2.4757-2.56420.29531310.22442522X-RAY DIFFRACTION83
2.5642-2.66680.25691240.21132326X-RAY DIFFRACTION78
2.6668-2.78820.26571360.20162482X-RAY DIFFRACTION83
2.7882-2.93520.20431480.17832835X-RAY DIFFRACTION91
2.9352-3.1190.24381510.17932829X-RAY DIFFRACTION92
3.119-3.35980.22511450.15882737X-RAY DIFFRACTION92
3.3598-3.69770.19121490.13472804X-RAY DIFFRACTION91
3.6977-4.23240.15391460.12852768X-RAY DIFFRACTION90
4.2324-5.3310.1881300.13422522X-RAY DIFFRACTION83
5.331-44.71150.24831500.18712827X-RAY DIFFRACTION93

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