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- PDB-3eoh: Refined group II intron structure -

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Basic information

Entry
Database: PDB / ID: 3eoh
TitleRefined group II intron structure
Components
  • 5'-R(*UP*UP*AP*UP*UP*A)-3'
  • Group IIC intron
KeywordsRNA / Ribonucleic acid / Intron / Group II / exon
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.125 Å
AuthorsToor, N. / Rajashankar, K. / Keating, K.S. / Pyle, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for exon recognition by a group II intron.
Authors: Toor, N. / Rajashankar, K. / Keating, K.S. / Pyle, A.M.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group IIC intron
B: 5'-R(*UP*UP*AP*UP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,59642
Polymers135,4902
Non-polymers1,10540
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-276 kcal/mol
Surface area56810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.092, 94.969, 225.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain Group IIC intron


Mass: 133652.156 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Oceanobacillus iheyensis sequence modified using PCR mutagenesis
#2: RNA chain 5'-R(*UP*UP*AP*UP*UP*A)-3'


Mass: 1838.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Exon-like oligonucleotide
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 6% PEG 3350, 150 mM magnesium acetate, 350 mM KCL, 50 mM Na-HEPES pH 7.0, 0.5 mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2magnesium acetate11
3KCL11
4Na-HEPES11
5spermine11
6PEG 33512
7magnesium acetate12
8KCL12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2007
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.125→43.705 Å / Num. obs: 34739

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.125→43.705 Å / SU ML: 0.43 / σ(F): 0.1 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 1644 4.97 %
Rwork0.2081 --
obs0.2095 33095 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.378 Å2 / ksol: 0.233 e/Å3
Refinement stepCycle: LAST / Resolution: 3.125→43.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8248 40 13 8301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049238
X-RAY DIFFRACTIONf_angle_d1.39714402
X-RAY DIFFRACTIONf_dihedral_angle_d28.4175327
X-RAY DIFFRACTIONf_chiral_restr0.0711924
X-RAY DIFFRACTIONf_plane_restr0.005381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.125-3.21680.28881130.23462174X-RAY DIFFRACTION80
3.2168-3.32060.25441300.21992502X-RAY DIFFRACTION92
3.3206-3.43930.22941260.20642520X-RAY DIFFRACTION93
3.4393-3.57690.23781420.20492591X-RAY DIFFRACTION96
3.5769-3.73960.22771370.1922636X-RAY DIFFRACTION97
3.7396-3.93670.21541370.18882643X-RAY DIFFRACTION97
3.9367-4.18310.21211380.19172644X-RAY DIFFRACTION97
4.1831-4.50580.23311390.19542688X-RAY DIFFRACTION97
4.5058-4.95870.2251440.19262728X-RAY DIFFRACTION99
4.9587-5.67490.22671450.18452746X-RAY DIFFRACTION99
5.6749-7.14470.22141450.19562778X-RAY DIFFRACTION99
7.1447-43.70920.25171480.24172801X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 19.0081 Å / Origin y: 85.9752 Å / Origin z: 364.6508 Å
111213212223313233
T0.4711 Å20.0299 Å2-0.0566 Å2-0.4869 Å2-0.0728 Å2--0.4547 Å2
L0.3644 °2-0.2099 °20.407 °2-0.5744 °2-0.4438 °2--0.6881 °2
S-0.1122 Å °-0.1137 Å °0.0825 Å °0.225 Å °0.085 Å °-0.1722 Å °-0.1804 Å °-0.0242 Å °0.0236 Å °
Refinement TLS groupSelection details: all

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