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- PDB-1x4t: Solution structure of Isy1 domain in hypothetical protein -

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Basic information

Entry
Database: PDB / ID: 1x4t
TitleSolution structure of Isy1 domain in hypothetical protein
Componentshypothetical protein LOC57905Hypothesis
KeywordsRNA BINDING PROTEIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


post-spliceosomal complex / Formation of TC-NER Pre-Incision Complex / mRNA Splicing - Major Pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / post-mRNA release spliceosomal complex / Prp19 complex / U2-type catalytic step 1 spliceosome / generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition ...post-spliceosomal complex / Formation of TC-NER Pre-Incision Complex / mRNA Splicing - Major Pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / post-mRNA release spliceosomal complex / Prp19 complex / U2-type catalytic step 1 spliceosome / generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / catalytic step 2 spliceosome / mRNA splicing, via spliceosome / nucleus
Similarity search - Function
Helix hairpin bin / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Helix hairpin bin domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-splicing factor ISY1 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHe, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of Isy1 domain in hypothetical protein
Authors: He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S.
History
DepositionMay 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2005Provider: 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
Remark 650HELIX Determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein LOC57905


Theoretical massNumber of molelcules
Total (without water)10,2251
Polymers10,2251
Non-polymers00
Water0
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
RepresentativeModel #1lowest energy

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Components

#1: Protein hypothetical protein LOC57905 / Hypothesis / Mus musculus adult male thymus cDNA / RIKEN full-length enriched library / clone:5830446M03 product: ...Mus musculus adult male thymus cDNA / RIKEN full-length enriched library / clone:5830446M03 product:hypothetical protein / full insert sequence


Mass: 10224.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell free protein synthesis / Gene: 5830446M03Rik / Plasmid: P041018-11 / References: UniProt: Q9D3E2, UniProt: Q69ZQ2*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: 0.8mM U-15, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O,10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / 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
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.863Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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