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- PDB-6t3s: Structure of Oceanobacillus iheyensis group II intron U-mutant (C... -

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Basic information

Entry
Database: PDB / ID: 6t3s
TitleStructure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon
ComponentsGroup IIC Intron Ribozyme
KeywordsRNA / Ribozyme / Self-splicing / Retrotransposition / Spliceosome
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsMarcia, M. / Pyle, A.M.
Funding support France, United States, 3items
OrganizationGrant numberCountry
Other governmentANR-10-INSB-05-02 France
Other governmentANR-10-LABX-49-01 France
Howard Hughes Medical Institute United States
CitationJournal: Nat Commun / Year: 2020
Title: Visualizing group II intron dynamics between the first and second steps of splicing.
Authors: Manigrasso, J. / Chillon, I. / Genna, V. / Vidossich, P. / Somarowthu, S. / Pyle, A.M. / De Vivo, M. / Marcia, M.
History
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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 / struct_conn
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_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group IIC Intron Ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,61032
Polymers129,2251
Non-polymers1,38531
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-232 kcal/mol
Surface area58020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.890, 95.240, 227.896
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 IIC Intron Ribozyme


Mass: 129225.484 Da / Num. of mol.: 1 / Fragment: domains 1-5 and 5'-exon / Mutation: C289U/C358U/G385A / Source method: obtained synthetically / Details: in vitro transcription system / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.77 Å3/Da / Density % sol: 67.41 % / Mosaicity: 0.17 °
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM Na-HEPES pH 7.0, 100 mM magnesium acetate, 150 mM sodium chloride, 4% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2013
RadiationMonochromator: SINGLE CRYSTAL SI(220) SIDE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.279→48.893 Å / Num. all: 30804 / Num. obs: 30804 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Rsym value: 0.074 / Net I/av σ(I): 4.7 / Net I/σ(I): 15.8 / Num. measured all: 201533
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.28-3.466.50.9950.82877744340.4671.1970.9952.599.8
3.46-3.676.90.5761.32890541860.2590.6810.5764.4100
3.67-3.926.70.312.32654539470.1410.3670.317.4100
3.92-4.236.40.2063.42348936970.0970.2470.20610.2100
4.23-4.646.90.1245.82339033900.0550.1450.12415.3100
4.64-5.186.60.0779.52050831040.0350.090.07721.3100
5.18-5.996.30.04914.31764327850.0230.0590.04928.399.7
5.99-7.336.50.04216.11515023330.0190.0490.04233.1100
7.33-10.3760.03417.81115218490.0160.040.03438.699.8
10.37-48.8935.50.03312.3597410790.0180.0410.03342.398.1

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Processing

Software
NameVersionClassification
XDSVERSION March 30, 2013data reduction
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.25data extraction
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FAX

4fax


Resolution: 3.28→48.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 42.364 / SU ML: 0.332 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.414
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1550 5 %RANDOM
Rwork0.1967 ---
obs0.1983 29194 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 393.41 Å2 / Biso mean: 132.249 Å2 / Biso min: 56.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å2-0 Å2-0 Å2
2---4.61 Å2-0 Å2
3---1.92 Å2
Refinement stepCycle: final / Resolution: 3.28→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8390 63 25 8478
Biso mean--94.68 91.15 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0119457
X-RAY DIFFRACTIONr_bond_other_d0.0030.023863
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.28314742
X-RAY DIFFRACTIONr_angle_other_deg1.6639399
X-RAY DIFFRACTIONr_chiral_restr0.1130.21570
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022082
LS refinement shellResolution: 3.28→3.363 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.36 110 -
Rwork0.346 2112 -
obs--99.46 %
Refinement TLS params.Method: refined / Origin x: -24.518 Å / Origin y: 8.55 Å / Origin z: -25.619 Å
111213212223313233
T0.4552 Å20.017 Å20.0563 Å2-0.4017 Å20.0292 Å2--0.3487 Å2
L0.7941 °20.9353 °2-0.8267 °2-2.2587 °2-0.7965 °2--1.2313 °2
S-0.2577 Å °0.3139 Å °-0.1398 Å °-0.8762 Å °0.1607 Å °-0.2034 Å °0.1962 Å °-0.0958 Å °0.097 Å °

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