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- PDB-1jwc: NMR SOLUTION STRUCTURE OF THE RNA HAIRPIN BINDING SITE FOR THE HI... -

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Basic information

Entry
Database: PDB / ID: 1jwc
TitleNMR SOLUTION STRUCTURE OF THE RNA HAIRPIN BINDING SITE FOR THE HISTONE STEM-LOOP BINDING PROTEIN
Components5'-R(*GP*GP*CP*CP*AP*AP*AP*GP*GP*CP*CP*CP*UP*UP*UP*UP*CP*AP*GP*GP*GP*CP*CP*AP*CP*CP*CP*A)-3'
KeywordsRNA / HAIRPIN / TETRALOOP / 3' STACK
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsDejong, E.S. / Marzluff, W.F. / Nikonowicz, E.P.
CitationJournal: RNA / Year: 2002
Title: NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein.
Authors: DeJong, E.S. / Marzluff, W.F. / Nikonowicz, E.P.
History
DepositionSep 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,9281
Polymers8,9281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

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


Mass: 8928.382 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY AT THE 3' END OF THE REPLICATION-DEPENDENT HISTONE MRNAS OF VERTEBRATES. THIS SEQUENCE CORRESPONDS TO THE MOUSE H4-12 GENE.
References: GenBank: 51308

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1213D 13C-separated NOESY
2323D 15N-separated NOESY
142DQF-COSY
152HETCOR
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING A VARIETY OF 2D AND 3D HOMO- AND HETERO-NUCLEAR NMR METHODS

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Sample preparation

CrystalDescription: THIS STRUCTURE WAS DETERMINED USING A VARIETY OF 2D AND 3D HOMO- AND HETERO-NUCLEAR NMR METHODS.
Details
Solution-IDContentsSolvent system
12.3 MM U-13C; 20 MM KPI, 20 MM KCL, 0.02 MM EDTA100% D2O
22.5 MM 15N-labeled; 20 MM KPI, 20 MM KCL, 0.02 MM EDTA100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM 6.8 ambient 301 K
2100 mM 6.8 ambient 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

SoftwareName: X-PLOR / Version: 3.851 / Classification: refinement
NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brunger, A.refinement
Felix980Biosymprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: CALCULATIONS WERE PERFORMED USING 232 CONFORMATIONALLY RESTRICTIVE NOE DERIVED DISTANCE CONSTRAINTS AND 55 BACKBONE AND 15 RIBOSE TORSION ANGLE CONSTRAINTS. BASE PAIR CONSTRAINTS WERE ...Details: CALCULATIONS WERE PERFORMED USING 232 CONFORMATIONALLY RESTRICTIVE NOE DERIVED DISTANCE CONSTRAINTS AND 55 BACKBONE AND 15 RIBOSE TORSION ANGLE CONSTRAINTS. BASE PAIR CONSTRAINTS WERE INTRODUCED FOR SIX BASE PAIRS USING HEAVY ATOM-HEAVY ATOM CONSTRAINTS. COORDINATES ARE FOR THE HAIRPIN DOMAIN ONLY. 5' FLANKING (GGCCAAA) AND 3' FLANKING (ACCCA) COORDINATES ARE NOT INCLUDED WITH THIS DEPOSITION. FEW CONSTRAINTS WERE OBTAINED FOR THESE VERY DYNAMIC REGIONS AND ALTHOUGH THEY WERE INCLUDED AS PART OF THE STRUCTURE CALCULATION, THEIR CONFORMATIONS APPEAR TO BE RANDOMLY DISTRIBUTED.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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