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- PDB-3igi: Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron -

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Basic information

Entry
Database: PDB / ID: 3igi
TitleTertiary Architecture of the Oceanobacillus Iheyensis Group II Intron
Components
  • 5'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-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. / Keating, K.S. / Fedorova, O. / Rajashankar, K. / Wang, J. / Pyle, A.M.
CitationJournal: Rna / Year: 2010
Title: Tertiary architecture of the Oceanobacillus iheyensis group II intron.
Authors: Toor, N. / Keating, K.S. / Fedorova, O. / Rajashankar, K. / Wang, J. / Pyle, A.M.
History
DepositionJul 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)139,59768
Polymers137,6682
Non-polymers1,93066
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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: Sequence modified from group IIC intron found naturally in Oceanobacillus Iheyensis
#2: RNA chain 5'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-3'


Mass: 4015.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Product of intron self-cleavage
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.47 Å3/Da / Density % sol: 64.57 %
Components of the solutions
IDConc.NameCrystal-IDSol-ID
110 mg/ml group II intron11
240 mM magnesium chloride11
35 mM sodium cacodylate pH 6.511
46% PEG 335012
5150mM magnesium acetate12
6350 mM KCl12
750 mM Na-HEPES pH 7.012
80.5 mM spermine13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.5418 Å
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 wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.125→43.705 Å / Num. obs: 34359 / Observed criterion σ(F): 0.1
Reflection shellResolution: 3.125→3.217 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXmodel building
PHENIX(phenix.refine: 1.4_70)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EOH

3eoh


Resolution: 3.125→43.705 Å / SU ML: 0.35 / σ(F): 0.1 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1644 4.97 %
Rwork0.1826 --
obs0.1844 33095 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.946 Å2 / ksol: 0.218 e/Å3
Refinement stepCycle: LAST / Resolution: 3.125→43.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8501 66 89 8656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079523
X-RAY DIFFRACTIONf_angle_d1.25914851
X-RAY DIFFRACTIONf_dihedral_angle_d20.2723954
X-RAY DIFFRACTIONf_chiral_restr0.1581978
X-RAY DIFFRACTIONf_plane_restr0.019395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1249-3.21680.28431130.22722174X-RAY DIFFRACTION80
3.2168-3.32060.2551300.22502X-RAY DIFFRACTION92
3.3206-3.43930.20731260.17752520X-RAY DIFFRACTION93
3.4393-3.57690.19731420.17132591X-RAY DIFFRACTION96
3.5769-3.73960.19131370.16732636X-RAY DIFFRACTION97
3.7396-3.93670.21421370.15822643X-RAY DIFFRACTION97
3.9367-4.18310.18541380.1582644X-RAY DIFFRACTION97
4.1831-4.50580.20871390.17042688X-RAY DIFFRACTION97
4.5058-4.95870.20881440.17032728X-RAY DIFFRACTION99
4.9587-5.67490.20341450.15462746X-RAY DIFFRACTION99
5.6749-7.14470.17481450.1622778X-RAY DIFFRACTION99
7.1447-43.70920.23411480.21232801X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 19.2457 Å / Origin y: 85.8177 Å / Origin z: 364.7161 Å
111213212223313233
T0.2586 Å20.0028 Å2-0.0565 Å2-0.3223 Å2-0.0846 Å2--0.2769 Å2
L0.2459 °2-0.171 °20.3141 °2-0.4576 °2-0.3605 °2--0.5895 °2
S-0.0973 Å °-0.0934 Å °0.07 Å °0.1808 Å °0.0634 Å °-0.1775 Å °-0.1498 Å °-0.0355 Å °0.0335 Å °
Refinement TLS groupSelection details: all

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