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- PDB-1q96: Crystal structure of a mutant of the sarcin/ricin domain from rat... -

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Basic information

Entry
Database: PDB / ID: 1q96
TitleCrystal structure of a mutant of the sarcin/ricin domain from rat 28S rRNA
Componentssarcin/ricin 28S rRNA
KeywordsRNA / sarcin/ricin domain / ribonucleic acid / RNA recognition / ribosomes / elongation factors / mutant / stem loop
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sarcin/ricin 28S rRNA
B: sarcin/ricin 28S rRNA
C: sarcin/ricin 28S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5187
Polymers26,1343
Non-polymers3844
Water5,513306
1
A: sarcin/ricin 28S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9033
Polymers8,7111
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sarcin/ricin 28S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8072
Polymers8,7111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: sarcin/ricin 28S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8072
Polymers8,7111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.246, 42.246, 336.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: RNA chain sarcin/ricin 28S rRNA


Mass: 8711.271 Da / Num. of mol.: 3 / Fragment: sarcin/ricin domain / Mutation: C13U, G18A / Source method: obtained synthetically
Details: THE 28S ribosomal RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE 28S ribosomal RNA IS NATURALLY FOUND IN Rattus rattus (RAT).
References: GenBank: 3891767
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, K-MOPS, magnesium chloride, spermine, cobalt chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2K-MOPS11
3magnesium chloride11
4spermine11
5cobalt chloride11
6H2O11
7ammonium sulfate12
8spermine12
9cobalt chloride12
10K-MOPS12
11H2O12
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
620 mM1reservoirMgCl2
71 mMspermine1reservoir
82 mM1reservoirCoCl2
91
101
111

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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: 1.75→40 Å / Num. all: 32531 / Num. obs: 29876 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 31.5
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2 / % possible all: 80
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 91.3 %
Reflection shell
*PLUS
% possible obs: 80 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 483D

483d


Resolution: 1.75→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2851 8.8 %Random
Rwork0.201 ---
all0.205 32531 --
obs0.205 28603 88 %-
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1872 20 306 2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.8934.5
X-RAY DIFFRACTIONc_mcangle_it3.5096
X-RAY DIFFRACTIONc_scbond_it3.2896
X-RAY DIFFRACTIONc_scangle_it3.9247.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna-allatom.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3SO4.param
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.294 / Rfactor Rwork: 0.269

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