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- PDB-4r0d: Crystal structure of a eukaryotic group II intron lariat -

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Basic information

Entry
Database: PDB / ID: 4r0d
TitleCrystal structure of a eukaryotic group II intron lariat
Components
  • GROUP IIB INTRON LARIAT
  • LIGATED EXONS
KeywordsRNA / lariat / ribozyme / 2'-5' phosphodiester
Function / homologyIRIDIUM HEXAMMINE ION / SPERMINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesPylaiella littoralis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.676 Å
AuthorsRobart, A.R. / Chan, R.T. / Peters, J.K. / Rajashankar, K.R. / Toor, N.
CitationJournal: Nature / Year: 2014
Title: Crystal structure of a eukaryotic group II intron lariat.
Authors: Robart, A.R. / Chan, R.T. / Peters, J.K. / Rajashankar, K.R. / Toor, N.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Oct 29, 2014Group: Source and taxonomy
Revision 1.4May 25, 2016Group: Source and taxonomy
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 IIB INTRON LARIAT
B: LIGATED EXONS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,496141
Polymers207,5192
Non-polymers13,977139
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15770 Å2
ΔGint-231 kcal/mol
Surface area96750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.639, 255.361, 136.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-745-

MG

21A-760-

MG

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain GROUP IIB INTRON LARIAT


Mass: 201158.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pylaiella littoralis (eukaryote) / Description: RNA was prepared by in vitro transcription / Production host: cell-free synthesis (others)
#2: RNA chain LIGATED EXONS


Mass: 6360.847 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pylaiella littoralis (eukaryote) / Description: RNA was prepared by in vitro transcription / Production host: cell-free synthesis (others)

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Non-polymers , 5 types, 254 molecules

#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical...
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: H18IrN6
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 83 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.44 Å3/Da / Density % sol: 64.27 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.4 mM spermine, 21% 2-Methyl-2,4-pentanediol, 175 mM magnesium acetate tetrahydrate, and 90 mM MES monohydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.1052, 1.3854, 1.3858
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.10521
21.38541
31.38581
ReflectionResolution: 3.676→81.82 Å / Num. all: 31207 / Num. obs: 31107 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rsym value: 0.149 / Net I/σ(I): 6.4
Reflection shellResolution: 3.68→3.74 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 0.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 3.676→81.82 Å / SU ML: 0.47 / σ(F): 1.33 / Phase error: 33.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2739 1994 6.41 %
Rwork0.2386 --
obs0.2411 31107 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.676→81.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 13472 393 115 13980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01715336
X-RAY DIFFRACTIONf_angle_d1.48324103
X-RAY DIFFRACTIONf_dihedral_angle_d19.4637572
X-RAY DIFFRACTIONf_chiral_restr0.0993148
X-RAY DIFFRACTIONf_plane_restr0.004628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6761-3.7680.37921160.36831730X-RAY DIFFRACTION83
3.768-3.86990.35111410.35992045X-RAY DIFFRACTION99
3.8699-3.98380.35121430.34812088X-RAY DIFFRACTION100
3.9838-4.11240.37311430.33052088X-RAY DIFFRACTION100
4.1124-4.25940.32331430.3242091X-RAY DIFFRACTION100
4.2594-4.42990.37121430.31542077X-RAY DIFFRACTION100
4.4299-4.63150.30321430.28522083X-RAY DIFFRACTION100
4.6315-4.87560.32021440.28592101X-RAY DIFFRACTION100
4.8756-5.18110.31521420.26172086X-RAY DIFFRACTION100
5.1811-5.5810.24721450.24762108X-RAY DIFFRACTION100
5.581-6.14250.27881460.2362120X-RAY DIFFRACTION100
6.1425-7.03090.26661450.23092132X-RAY DIFFRACTION100
7.0309-8.85650.24381470.22632144X-RAY DIFFRACTION100
8.8565-81.83970.23231530.17462220X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.7416 Å / Origin y: 32.5694 Å / Origin z: -10.463 Å
111213212223313233
T0.4705 Å2-0.2475 Å2-0.2035 Å2-0.767 Å20.0908 Å2--0.6735 Å2
L0.4804 °2-0.084 °2-0.5721 °2-0.3573 °2-0.0009 °2--1.6533 °2
S-0.1017 Å °-0.226 Å °-0.1083 Å °-0.0794 Å °0.099 Å °-0.1781 Å °-0.3313 Å °0.7438 Å °-0.008 Å °
Refinement TLS groupSelection details: all

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