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- PDB-1whn: Solution structure of the dsRBD from hypothetical protein BAB26260 -

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Entry
Database: PDB / ID: 1whn
TitleSolution structure of the dsRBD from hypothetical protein BAB26260
Componentshypothetical protein RIKEN cDNA 2310016K04
KeywordsRNA BINDING PROTEIN / double-stranded RNA binding domain / dsRBD / DSRM / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / : / protein kinase inhibitor activity / NADPH binding / double-stranded RNA binding / FMN binding / flavin adenine dinucleotide binding ...tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / : / protein kinase inhibitor activity / NADPH binding / double-stranded RNA binding / FMN binding / flavin adenine dinucleotide binding / endoplasmic reticulum / mitochondrion / cytoplasm / cytosol
Similarity search - Function
tRNA-dihydrouridine synthase / 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 ...tRNA-dihydrouridine synthase / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsNagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the dsRBD from hypothetical protein BAB26260
Authors: Nagata, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein RIKEN cDNA 2310016K04


Theoretical massNumber of molelcules
Total (without water)14,2171
Polymers14,2171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein hypothetical protein RIKEN cDNA 2310016K04


Mass: 14217.239 Da / Num. of mol.: 1 / Fragment: double-stranded RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: RIKEN cDNA 2310016K04 / Plasmid: P021209-40 / References: UniProt: Q9D7B1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.28mM PROTEIN U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.4Johnsondata analysis
CYANA2Guentertstructure solution
NMRPipe2.3Delaglioprocessing
KUJIRA0.901Kobayashi, N.data analysis
CYANA2Guentertrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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