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- PDB-480d: CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA -

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Basic information

Entry
Database: PDB / ID: 480d
TitleCRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA
ComponentsSARCIN/RICIN DOMAIN FROM 23 S RRNA
KeywordsRNA / SARCIN/RICIN LOOP OR DOMAIN / RNA RECOGNITION / RIBOSOMES / ELONGATION FACTORS
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 20, 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 DOMAIN FROM 23 S RRNA


Theoretical massNumber of molelcules
Total (without water)8,7441
Polymers8,7441
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.95, 29.95, 76.42
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Cell settingtetragonal
Space group name H-MP43

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Components

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


Mass: 8744.255 Da / Num. of mol.: 1 / Fragment: SARCIN/RICIN DOMAIN / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.04 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.0 - 3.2 M (NH4)2SO4, BUFFER X (50 MM POTASIUM MOPS, PH 7.0; 10 MM MGCL2; AND 10 MM MNCL2), AND ~2.5 MG/ML RNA, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2POTASIUM MOPS11
3MGCL211
4MNCL211
5(NH4)2SO412
6POTASIUM MOPS12
7MGCL212
8MNCL212
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
81

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 12, 1998
RadiationMonochromator: MSC MIRROR BOX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 10744 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 35.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.459 / % possible all: 98.5
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE RELATED RAT SARCIN/RICIN STRUCTURE (430D)

430d


Resolution: 1.5→20 Å / Cross valid method: R FREE / σ(F): 0 / σ(I): 0
Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN: ACTA CRYST.D, 52, 57 (1996)
Details: AFTER BULK SOLVENT CORRECTION AND ANISOTROPIC SCALING OF FOBS, CYCLES OF POWELL MINIMIZATION FOLLOWED BY B-FACTOR REFINEMENT WERE DONE.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1075 9.9 %10% OF DATA THAT WAS RANDOMLY SELECTED. OVERALL R FOR ALL DATA WAS NEVER CALCULATED
Rwork0.1798 ---
all0.18 10535 --
obs0.18 10535 96.8 %-
Displacement parametersBiso mean: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 579 0 84 663
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.832
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.5→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 39 7.5 %
Rwork0.336 420 -
obs--88 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1
LS refinement shell
*PLUS
Rfactor Rfree: 0.33 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.336 / Rfactor obs: 0.336

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