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- PDB-2i7z: GAAA tetraloop receptor complex with associated manganese ions. -

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Basic information

Entry
Database: PDB / ID: 2i7z
TitleGAAA tetraloop receptor complex with associated manganese ions.
Components43-MER
KeywordsRIBONUCLEIC ACID / GAAA tetraloop / 11-nucleotide receptor / RNA tertiary structure
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Structures were refined by cooling from 3000 K to 100 K in 58 cycles of restrained Cartesian coordinate space corresponding to a total of 28 ps. The force constant for RDCs was increased from 0.001 to 0.2 kcal mol-1 Hz-2. Five hundred steps of energy minimization using the Powell algorithm followed simulated annealing.
AuthorsDavis, J.H. / Butcher, S.E.
CitationJournal: Rna / Year: 2007
Title: Role of metal ions in the tetraloop-receptor complex as analyzed by NMR.
Authors: Davis, J.H. / Foster, T.R. / Tonelli, M. / Butcher, S.E.
History
DepositionAug 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 43-MER
B: 43-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,29612
Polymers27,7472
Non-polymers54910
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 43-MER


Mass: 13873.258 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: GAAA tetraloop and 11-nt receptor sequences are found in Group I and Group II introns
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1342D NOESY
1442D TOCSY
256H 1D
2662D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM GAAA tetraloop receptor RNA, 10 uM manganese, 12 mM MgCl2 50 mM NaCl; 100% D2O100% D2O
21 mM GAAA tetraloop receptor RNA, 50 uM manganese, 12 mM MgCl2 50 mM NaCl; 100% D2O100% D2O
31 mM GAAA tetraloop receptor RNA, 100 uM manganese, 12 mM MgCl2 50 mM NaCl; 100% D2O100% D2O
41 mM GAAA tetraloop receptor RNA, 500 uM manganese, 12 mM MgCl2 50 mM NaCl; 100% D2O100% D2O
51 mM GAAA tetraloop receptor RNA, 100 uM manganese, 12 mM MgCl2 50 mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
61 mM GAAA tetraloop receptor RNA, 500 uM manganese, 12 mM MgCl2 50 mM NaCl90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.0 ambient 303 K
27.0 ambient 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger A. T. etalrefinement
X-PLOR2.11refinement
XwinNMR2.6processing
Sparky3.111data analysis
RefinementMethod: Structures were refined by cooling from 3000 K to 100 K in 58 cycles of restrained Cartesian coordinate space corresponding to a total of 28 ps. The force constant for RDCs was increased from ...Method: Structures were refined by cooling from 3000 K to 100 K in 58 cycles of restrained Cartesian coordinate space corresponding to a total of 28 ps. The force constant for RDCs was increased from 0.001 to 0.2 kcal mol-1 Hz-2. Five hundred steps of energy minimization using the Powell algorithm followed simulated annealing.
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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