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- PDB-2fb7: NMR Solution Structure of protein from Zebra Fish Dr.13312 -

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Basic information

Entry
Database: PDB / ID: 2fb7
TitleNMR Solution Structure of protein from Zebra Fish Dr.13312
ComponentsSm-like protein, LSm-14_N (RAP55)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Dr.13312 / BC055387 / AAH55387 / LSm14_N / RAP55 / Sm-like protein / strongly bent five-stranded antiparallel beta-sheet / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


P-body assembly / stress granule assembly / P-body / mRNA binding
Similarity search - Function
FFD box / TFG box / FFD box profile. / TFG box profile. / Lsm14-like, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain ...FFD box / TFG box / FFD box profile. / TFG box profile. / Lsm14-like, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
LSM14 homolog A (SCD6, S. cerevisiae) / Lsm14a protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, water refinement
AuthorsTyler, R.C. / Song, J. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: NMR Solution Structure of protein from Zebra Fish Dr.13312
Authors: Tyler, R.C. / Song, J. / Markley, J.L.
History
DepositionDec 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Sm-like protein, LSm-14_N (RAP55)


Theoretical massNumber of molelcules
Total (without water)10,7041
Polymers10,7041
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)10 / 100fewest violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Sm-like protein, LSm-14_N (RAP55)


Mass: 10704.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: BC055387 / Plasmid: PEU-HIS / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q7SXR4, UniProt: Q6P111*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
NMR detailsText: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING A CRYOGENIC PROBE.

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Sample preparation

DetailsContents: 0.46 MM PROTEIN, 100 MM NACL, 10 MM BIS-TRIS, 5 MM DTT, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 7 / Pressure: ambient / Temperature: 289 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameClassification
CNSrefinement
NMRPIPE 97.027.12.56., NMRVIEW 5.0.4, ARIA 1.2, CNS 1.1data collection
RefinementMethod: simulated annealing, torsion angle dynamics, water refinement
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 1106 NOE RESTRAINTS (974 UNAMBIGUOUS, 132 AMBIGUOUS), 40 HBOND RESTRAINTS, AND 172 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: fewest violations / Conformers calculated total number: 100 / Conformers submitted total number: 10

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