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- PDB-1d0t: SOLUTION STRUCTURE OF A PHOSPHOROTHIOATE MODIFIED RNA BINDING SIT... -

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Basic information

Entry
Database: PDB / ID: 1d0t
TitleSOLUTION STRUCTURE OF A PHOSPHOROTHIOATE MODIFIED RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN
ComponentsPHOSPHOROTHIOATE SUBSTITUTED PHAGE MS2 RNA BINDING SITE
KeywordsRNA / RNA HAIRPIN / PHOSPHOROTHIOATE / THIOPHOSPHATE / BULGED BASE / STEM-LOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics refinement
Model type detailsminimized average
AuthorsSmith, J.S. / Nikonowicz, E.P.
CitationJournal: Biochemistry / Year: 2000
Title: Phosphorothioate substitution can substantially alter RNA conformation.
Authors: Smith, J.S. / Nikonowicz, E.P.
History
DepositionSep 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4May 22, 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: PHOSPHOROTHIOATE SUBSTITUTED PHAGE MS2 RNA BINDING SITE


Theoretical massNumber of molelcules
Total (without water)6,8091
Polymers6,8091
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 / 30back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain PHOSPHOROTHIOATE SUBSTITUTED PHAGE MS2 RNA BINDING SITE


Mass: 6809.375 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Transcription by T7 RNA ploymerase using 5'-a-thio-ATP

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
2323D 15N-separated NOESY
242DQF-COSY
25231P-1H HETCOR
2622D 13C-filtered NOESY
NMR detailsText: The structure was determined using standard 2D homonuclear and 2D/3D heteronuclear techniques. Filtered experiments used to identify inter-residue NOEs involving unlabeled A residues

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA90% H2O/10% D2O
22.0 mM replicase operator RNA U-15N,13C at U, C, and G, unlabeled A; phosphorothioate 5' to each adenine;; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA100% D2O
Sample conditionsIonic strength: ~50mM / pH: 6.8 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR1994Spectraspincollection
Felix1998Biosym-MSIprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing, molecular dynamics refinement / Software ordinal: 1
Details: structures were calculated using 313 conformationally restrictive NOE distance constraints (i.e., intra-residue sugar-sugar NOEs are not included), 20 H-bond base pair constraints, 30 ...Details: structures were calculated using 313 conformationally restrictive NOE distance constraints (i.e., intra-residue sugar-sugar NOEs are not included), 20 H-bond base pair constraints, 30 backbone dihedral restraints, and dihedral restraints to restrict sugar pucker conformation. Parameter file was modified to incorporate bond-length, bond-angle, charge, van der Waal's radius for the Rp phosphoryl sulfur atoms located 5' to each adenine in the sequence. [Jaroszewski, JW., et al., Anti-Cancer Drug Design ( 1992) 7, 253; Florian, J. et al., J. Am. Chem. Soc. (1998) 120, 7959].
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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