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- PDB-483d: CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA -

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Basic information

Entry
Database: PDB / ID: 483d
TitleCRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA
ComponentsSARCIN/RICIN RRNA DOMAIN
KeywordsRNA / SACIN/RICIN DOMAIN RNA RECOGNITION RIBOSOMES ELONGATION FACTORS CRYSTAL STRUCTURE
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsCorrell, C.C. / Wool, I.G. / Munishkin, A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution.
Authors: Correll, C.C. / Wool, I.G. / Munishkin, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal Structure of the Ribosomal RNA Domain Essential for Binding Elongation Factors
Authors: Correll, C.C. / Munishkin, A. / Chan, Y.-L. / Ren, Z. / Wool, I.G.
#2: Journal: Biophys.J. / Year: 1999
Title: Comparison of the Crystal and Solution Structures of Two RNA Oligonucleotides
Authors: Rife, J.P. / Stallings, S.G. / Correll, C.C. / Dallas, A. / Steitz, T.A. / Moore, P.B.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: The Sarcin/Ricin Loop, a Modular RNA
Authors: Szewczak, A.A. / Moore, P.B.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: The Conformation of the Sarcin/Ricin Loop from 28 S Ribosomal RNA
Authors: Szewczak, A.A. / Moore, P.B.
History
DepositionJul 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SARCIN/RICIN RRNA DOMAIN


Theoretical massNumber of molelcules
Total (without water)8,7441
Polymers8,7441
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.481, 29.481, 76.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43

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Components

#1: RNA chain SARCIN/RICIN RRNA DOMAIN


Mass: 8744.255 Da / Num. of mol.: 1 / Fragment: 27 NA LONG SARCIN/RICIN DOMAIN / Source method: obtained synthetically
Details: SEQUENCE OCCURS NATURALLY IN E.COLI 28 S RIBOSOMAL RNA
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.97 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 3.0 - 3.2 M (NH4)2SO4, (50 MM KMOPS, 10 MM MGCL2, 10MM MNCL2), 2.5 MG/ML RNA, pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1KMOPS11
2MGCL211
3MNCL211
4(NH4)2SO411
5(NH4)2SO412
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlprotein1drop
21.0 mMNa-EDTA1drop
310 mMTris1drop
43.0-3.2 Mammonium sulfate1reservoir
550 mMpotassium MOPS1reservoir
610 mM1reservoirMgCl2
710 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9188
DetectorType: ADSC / Detector: CCD / Date: May 14, 1998 / Details: BENT CYLINDRICAL SI-MIRROR
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 1.11→20 Å / Num. obs: 25407 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 35.4
Reflection shellResolution: 1.11→1.12 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.487 / % possible all: 2.3
Reflection
*PLUS
Highest resolution: 1.11 Å / Lowest resolution: 20 Å / Observed criterion σ(I): -3 / Redundancy: 4.7 %
Reflection shell
*PLUS
% possible obs: 84.5 % / Redundancy: 2.2 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE RELATED RAT SARCIN/RICIN STRUCTURE (430D)

430d


Resolution: 1.11→20 Å / Num. parameters: 7554 / Num. restraintsaints: 10247 / Cross valid method: FREE R / σ(F): 0
Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN: ACTA CRYST.D, 52, 57 (1996)
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995) 53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1267 5.3 %RANDOM
all0.156 23932 --
obs0.152 -97.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 732
Refinement stepCycle: LAST / Resolution: 1.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 682 0 155 837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.006
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.027
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5.3 % / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.029
X-RAY DIFFRACTIONs_angle_d0.035
LS refinement shell
*PLUS
Rfactor obs: 0.295

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