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- PDB-2cq2: solution structure of RNA binding domain in Hypothetical protein ... -

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Basic information

Entry
Database: PDB / ID: 2cq2
Titlesolution structure of RNA binding domain in Hypothetical protein LOC91801
Componentshypothetical protein LOC91801
KeywordsRNA BINDING PROTEIN / RRM domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tRNA (carboxymethyluridine34-5-O)-methyltransferase / tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity / tRNA (uridine) methyltransferase activity / tRNA wobble uridine modification / tRNA modification in the nucleus and cytosol / tRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / 2-oxoglutarate-dependent dioxygenase activity / tRNA binding / iron ion binding ...tRNA (carboxymethyluridine34-5-O)-methyltransferase / tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity / tRNA (uridine) methyltransferase activity / tRNA wobble uridine modification / tRNA modification in the nucleus and cytosol / tRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / 2-oxoglutarate-dependent dioxygenase activity / tRNA binding / iron ion binding / DNA damage response / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alkylated DNA repair protein AlkB, homologue 8, N-terminal / ALKBH8, RNA recognition motif / Alkylated DNA repair protein alkB homolog 8, N-terminal / : / Methyltransferase type 11 / Methyltransferase domain / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. ...Alkylated DNA repair protein AlkB, homologue 8, N-terminal / ALKBH8, RNA recognition motif / Alkylated DNA repair protein alkB homolog 8, N-terminal / : / Methyltransferase type 11 / Methyltransferase domain / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkylated DNA repair protein alkB homolog 8 / Alkylated DNA repair protein alkB homolog 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTsuda, K. / 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 RNA binding domain in Hypothetical protein LOC91801
Authors: Tsuda, K. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 LOC91801


Theoretical massNumber of molelcules
Total (without water)12,2691
Polymers12,2691
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, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein hypothetical protein LOC91801 / Hypothetical protein BC015183


Mass: 12268.832 Da / Num. of mol.: 1 / Fragment: RNA recognition motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: LOC9180 / Plasmid: P041012-04 / References: UniProt: Q8N989, UniProt: Q96BT7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.16mM 13C/15N-PROTEIN, 20mM d-Tris-HCl (pH 7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, Fprocessing
NMRView5.0.4Johnson, B.Adata analysis
KUJIRA0.9297Kobayashi, Ndata analysis
CYANA2.0.17Guntert, Pstructure solution
CYANA2.0.17Guntert, Prefinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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