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- PDB-1kks: Structure of the histone mRNA hairpin required for cell cycle reg... -

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Basic information

Entry
Database: PDB / ID: 1kks
TitleStructure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression
Components5'-R(*GP*GP*AP*AP*GP*GP*CP*CP*CP*UP*UP*UP*UP*CP*AP*GP*GP*GP*CP*CP*AP*CP*CP*C)-3'
KeywordsRNA / RNA HAIRPIN / HISTONE mRNA / RNA PROCESSING
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Molecular Dynamics, Simulated Annealing
AuthorsZanier, K. / Luyten, I. / Crombie, C. / Muller, B. / Schuemperli, D. / Linge, J.P. / Nilges, M. / Sattler, M.
CitationJournal: RNA / Year: 2002
Title: Structure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression.
Authors: Zanier, K. / Luyten, I. / Crombie, C. / Muller, B. / Schumperli, D. / Linge, J.P. / Nilges, M. / Sattler, M.
History
DepositionDec 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*AP*AP*GP*GP*CP*CP*CP*UP*UP*UP*UP*CP*AP*GP*GP*GP*CP*CP*AP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,6601
Polymers7,6601
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)15 / 100back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #8lowest energy

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Components

#1: RNA chain 5'-R(*GP*GP*AP*AP*GP*GP*CP*CP*CP*UP*UP*UP*UP*CP*AP*GP*GP*GP*CP*CP*AP*CP*CP*C)-3'


Mass: 7659.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence comes from the Histone H4-12 gene of Mus musculus. In vitro transcription using T7 RNA polymerase.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C HMQC-NOESY
1213D (H)CCH-E.COSY
1313D HCC-TOCSY-CCH-E.COSY
141spin echo difference CT-HSQC
252HNN-COSY
NMR detailsText: The structure was determined using standard heteronuclear triple resonance experiments

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N/13C 24mer RNA100% D2O
21 mM U-15N 24mer RNA10% D2O / 90% H2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM sodium phosphate, 0.1 mM EDTA 6.0 ambient 298 K
210 mM sodium phosphate, 0.1 mM EDTA 6.0 ambient 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker, Germanycollection
NMRPipe1.8Delaglio et al.processing
XEASY1.2Bartels et al.data analysis
ARIA/CNS1Linge, Nilgesstructure solution
Amber6Case et al.refinement
RefinementMethod: Molecular Dynamics, Simulated Annealing / Software ordinal: 1
Details: The structures are calculated with 451 distance restraints, 23 hydrogen bond restraints and 158 torsion angle restraints. The structures were calculated in ARIA/CNS and refined using AMBER.
NMR representativeSelection criteria: lowest energy
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: 100 / Conformers submitted total number: 15

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