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- PDB-1q9a: Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA... -

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Basic information

Entry
Database: PDB / ID: 1q9a
TitleCrystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution
ComponentsSarcin/ricin 23S rRNA
KeywordsRNA / sarcin/ricin domain / ribonucleic acid / RNA recognition / high resolution / ribosomes
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.04 Å
AuthorsCorrell, C.C. / Beneken, J. / Plantinga, M.J. / Lubbers, M. / Chan, Y.L.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: The common and distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure
Authors: Correll, C.C. / Beneken, J. / Plantinga, M.J. / Lubbers, M. / Chan, Y.L.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 23S rRNA


Theoretical massNumber of molelcules
Total (without water)8,7441
Polymers8,7441
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.529, 29.529, 76.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: RNA chain Sarcin/ricin 23S rRNA


Mass: 8744.255 Da / Num. of mol.: 1 / Fragment: sarcin/ricin domain / Source method: obtained synthetically
Details: THE 23S ribosomal RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE 23S ribosomal RNA IS NATURALLY FOUND IN Escherichia coli (bacteria).
References: GenBank: 26111017
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.91 Å3/Da / Density % sol: 35.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, K-MOPS, magnesium chloride, manganese chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2K-MOPS11
3magnesium chloride11
4manganese chloride11
5H2O11
6ammonium sulfate12
7K-MOPS12
8magnesium chloride12
9manganese chloride12
10H2O12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mg/mlRNA1drop
250 mMpotassium MOPS1droppH7.0
35 mM1dropMgCl2
43.0-3.2 Mammonium sulfate1reservoir
550 mMpotassium MOPS1reservoirpH7.0
610 mM1reservoirMgCl2
710 mM1reservoirMnCl2
81
91
101

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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 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97764 Å / Relative weight: 1
ReflectionResolution: 1.04→40 Å / Num. all: 31452 / Num. obs: 29848 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 55.3
Reflection shellResolution: 1.04→1.06 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2 / % possible all: 82.5
Reflection shell
*PLUS
% possible obs: 82.5 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXSphasing
SHELXL-97refinement
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.04→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1774 2981 random
Rwork0.1361 --
all0.1477 --
obs0.1477 29814 -
Refinement stepCycle: LAST / Resolution: 1.04→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 708 0 179 887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.023
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_mcbond_it
X-RAY DIFFRACTIONs_scbond_it
X-RAY DIFFRACTIONs_mcangle_it
X-RAY DIFFRACTIONs_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.319

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