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- PDB-5j02: Structure of the lariat form of a chimeric derivative of the Ocea... -

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Basic information

Entry
Database: PDB / ID: 5j02
TitleStructure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon.
Components
  • 5' EXON ANALOG (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3')
  • GROUP II INTRON LARIAT
KeywordsRNA / group II intron / lariat / 2'-5' phosphodiester bond / ribozyme / RNA catalysis / self-splicing
Function / homologyAMMONIUM ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.493 Å
AuthorsCosta, M. / Walbott, H. / Monachello, D. / Westhof, E. / Michel, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-BLAN-1502 France
CitationJournal: Science / Year: 2016
Title: Crystal structures of a group II intron lariat primed for reverse splicing.
Authors: Costa, M. / Walbott, H. / Monachello, D. / Westhof, E. / Michel, F.
History
DepositionMar 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.4Jan 10, 2024Group: 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_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GROUP II INTRON LARIAT
B: 5' EXON ANALOG (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,17662
Polymers137,7812
Non-polymers1,39660
Water3,081171
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-398 kcal/mol
Surface area61940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.020, 100.600, 220.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain GROUP II INTRON LARIAT


Mass: 135623.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#2: RNA chain 5' EXON ANALOG (5'-R(*CP*UP*GP*UP*UP*AP*(5MU))-3')


Mass: 2157.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5MU lacking 3'O / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 301.15 K / Method: vapor diffusion, sitting drop
Details: 50 mM Na-Cacodylate pH 6.5, 225 mM NH4Cl, 115 mM MgCl2, 22% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 24666 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 22.2 % / Biso Wilson estimate: 125.87 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.202 / Rrim(I) all: 0.207 / Χ2: 1.023 / Net I/σ(I): 12.32 / Num. measured all: 548093
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.49-3.5820.42.9911.235456180617370.7533.06796.2
3.58-3.682.5131.6340533174117410.8312.569100
3.68-3.791.6932.4739565170817080.9221.731100
3.79-3.911.4522.8137575166616660.91.486100
3.91-4.031.2393.437483162516250.9231.267100
4.03-4.171.0154.2434968152915290.9541.038100
4.17-4.330.815.3333468149714970.9640.829100
4.33-4.510.6736.3632926147314730.9750.689100
4.51-4.710.5148.0831902140314030.990.526100
4.71-4.940.39510.2729614132813280.990.405100
4.94-5.210.3212.9329047127212720.9930.327100
5.21-5.520.22717.0127010120712070.9960.233100
5.52-5.90.1820.225828115711570.9970.185100
5.9-6.380.16521.3723743106610660.9980.168100
6.38-6.990.13824.66220569839830.9980.141100
6.99-7.810.130.24198929189180.9980.102100
7.81-9.020.09133.6167557907900.9980.093100
9.02-11.050.06637.99139446976970.9990.068100
11.05-15.620.04751.82106045485480.9990.048100
15.620.03560572433332110.03696.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FAW

4faw


Resolution: 3.493→49.041 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 1232 5 %
Rwork0.2029 23396 -
obs0.2041 24628 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 477.94 Å2 / Biso mean: 146.0254 Å2 / Biso min: 44.54 Å2
Refinement stepCycle: final / Resolution: 3.493→49.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 9043 60 171 9274
Biso mean--155.87 137.58 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410367
X-RAY DIFFRACTIONf_angle_d0.38316276
X-RAY DIFFRACTIONf_chiral_restr0.0182102
X-RAY DIFFRACTIONf_plane_restr0.001421
X-RAY DIFFRACTIONf_dihedral_angle_d11.9645034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.493-3.63280.39091300.35062466259697
3.6328-3.79810.30291340.29225592693100
3.7981-3.99820.2961360.26525862722100
3.9982-4.24860.25371360.235325762712100
4.2486-4.57640.25341360.22325812717100
4.5764-5.03650.22261370.209926062743100
5.0365-5.76430.20141370.183425982735100
5.7643-7.25870.19871390.184826442783100
7.2587-49.04550.19641470.165227802927100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35150.10390.89622.18910.141.1794-0.2005-0.27070.08520.1609-0.17580.0482-0.4032-0.14930.25910.7715-0.0019-0.06420.71260.11430.6713201.5714211.284237.2165
22.67770.09520.06082.8083-0.59613.5316-0.22220.2009-0.2633-0.59420.0277-1.04510.39790.62610.08231.2081-0.20520.17580.92560.09971.6329213.7776214.8525222.9895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 419)A1 - 419
2X-RAY DIFFRACTION2(chain 'B' and resid -7 through -1)B-7 - -1

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