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- PDB-2k4c: tRNAPhe-based homology model for tRNAVal refined against base N-H... -

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Basic information

Entry
Database: PDB / ID: 2k4c
TitletRNAPhe-based homology model for tRNAVal refined against base N-H RDCs in two media and SAXS data
Components76-MER
KeywordsRNA / tRNAVal / RDC / SAXS / NCS
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing, torsion angle dynamics
AuthorsGrishaev, A. / Ying, J. / Canny, M.D. / Pardi, A. / Bax, A.
Citation
Journal: J.Biomol.Nmr / Year: 2008
Title: Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data.
Authors: Grishaev, A. / Ying, J. / Canny, M.D. / Pardi, A. / Bax, A.
#1: Journal: J.Biomol.NMR / Year: 2007
Title: Magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field
Authors: Ying, J. / Grishaev, A. / Latham, M. / Pardi, A. / Bax, A.
History
DepositionJun 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 24, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / ndb_struct_na_base_pair ...entity_src_gen / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref / struct_ref_seq
Item: _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num ..._entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: 76-MER


Theoretical massNumber of molelcules
Total (without water)24,4841
Polymers24,4841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 3structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 76-MER


Mass: 24483.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: sample is uniformly 15N labeled / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: GenBank: 1845291569

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N TROSY-HSQC
1212D 1H-15N HSQC
1312D 1H-15N TROSY-HSQC
1412D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] RNA (76-MER), 10 mM sodium phosphate, 80 mM sodium chloride, 5 mM magnesium chloride, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.41 mM [U-100% 15N] RNA (76-MER), 10 mM sodium phosphate, 150 mM sodium chloride, 5 mM magnesium chloride, 0.1 mM EDTA, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMRNA (76-MER)[U-100% 15N]1
10 mMsodium phosphate1
80 mMsodium chloride1
5 mMmagnesium chloride1
0.1 mMEDTA1
0.41 mMRNA (76-MER)[U-100% 15N]2
10 mMsodium phosphate2
150 mMsodium chloride2
5 mMmagnesium chloride2
0.1 mMEDTA2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1556.8ambient atm298 K
20.2257ambient atm298 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.9.14Schwieters, Kuszewski, Tjandra and Clorerefinement
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: tRNAVal solution structure is obtained by refinement of the tRNAPhe based homology model against RDC data (base N-H RDCs) from Pf1 and self-alignment (MSA), and SAXS data. Totals of 24 Pf1 ...Details: tRNAVal solution structure is obtained by refinement of the tRNAPhe based homology model against RDC data (base N-H RDCs) from Pf1 and self-alignment (MSA), and SAXS data. Totals of 24 Pf1 RDCs and 20 MSA RDcs were fitted. During the refinement, the local geometry was kept close to the tRNAPhe based homology model using a set of non-crystallographic symmetry restraint terms. The NCS potentials included: 70 sequential i/i+1 terms and 34 additional terms for base pairs and triplets. The experimental SAXS data between q=0.03 and 0.35 A^-1 were fitted as well.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3 / Conformers submitted total number: 1

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