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- PDB-1msy: GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA -

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Basic information

Entry
Database: PDB / ID: 1msy
TitleGUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA
ComponentsSARCIN/RICIN DOMAIN FROM 23 S RRNA
KeywordsRNA / A-minor motif / sarcin/ricin loop / RNA structure / RNA tertiary contacts / RNA motifs / conformational change / RNA-protein recognition / hydration
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsCorrell, C.C. / Swinger, K.
CitationJournal: RNA / Year: 2003
Title: Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution
Authors: Correll, C.C. / Swinger, K.
History
DepositionSep 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND A CRYSTALLOGRAPHIC TWO-FOLD AXIS PASSES THROUGH THE TERMINAL GU WOBBLEBASE PAIR. EACH ...COMPOUND A CRYSTALLOGRAPHIC TWO-FOLD AXIS PASSES THROUGH THE TERMINAL GU WOBBLEBASE PAIR. EACH MOLECULE ABOUT THE 2-FOLD CONTRIBUTES ONE NUCLEOTIDE TO THE WOBBLE PAIR AND THE NUCLEOTIDE THAT COULD FORM THE INTRAMOLECULAR CLOSING PAIR IS DISORDERED. NOTE THAT THE OCCUPANCIES FOR THESE NUCLEOTIDES IS 0.5.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SARCIN/RICIN DOMAIN FROM 23 S RRNA


Theoretical massNumber of molelcules
Total (without water)8,7051
Polymers8,7051
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.974, 22.534, 58.465
Angle α, β, γ (deg.)90.00, 101.72, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2647-

U

21A-2673-

G

31A-3002-

HOH

41A-3004-

HOH

51A-3068-

HOH

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Components

#1: RNA chain SARCIN/RICIN DOMAIN FROM 23 S RRNA


Mass: 8705.215 Da / Num. of mol.: 1 / Mutation: A2660U, G2661A / Source method: obtained synthetically
Details: A2660U and G2661U double mutant of the SRL domain from E.coli rRNA
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, potassium MOPS, magnesium chloride, manganese chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2potassium MOPS11
3MgCl211
4MnCl211
5(NH4)2SO412
6MgCl212
7MnCl212
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mg/mlprotein1drop
21.0 mMsodium EDTA1drop
310 mMTris1droppH8.0
43.0-3.2 Mammonium sulfate1reservoir
550 mMpotassium MOPS1reservoirpH7.0
610 mM1reservoirMgCl2
710 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97764 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 6, 2000
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97764 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 14372 / Num. obs: 14372 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 21.8
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.323 / % possible all: 80
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 40 Å
Reflection shell
*PLUS
% possible obs: 80 %

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 483D

483d


Resolution: 1.41→29 Å / Num. parameters: 6236 / Num. restraintsaints: 8182 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1419 11 %RANDOM
Rwork0.164 ---
all0.1637 14372 --
obs0.1637 14372 97.9 %-
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 662.5
Refinement stepCycle: LAST / Resolution: 1.41→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 582 0 109 691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0195
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.006
X-RAY DIFFRACTIONs_approx_iso_adps0.079
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.42 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_bond_d / Dev ideal: 0.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.458 / Rfactor Rwork: 0.278

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