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- PDB-6t3k: Structure of Oceanobacillus iheyensis group II intron G-mutant (C... -

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Basic information

Entry
Database: PDB / ID: 6t3k
TitleStructure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon
Components(Group IIC Intron ...) x 2
KeywordsRNA / Ribozyme / Self-splicing / Retrotransposition / Spliceosome
Function / homology: / SPERMINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 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 / pdbx_struct_conn_angle / struct_conn
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.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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group IIC Intron Ribozyme
B: Group IIC Intron Ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,09852
Polymers129,2352
Non-polymers2,86350
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-267 kcal/mol
Surface area56780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.659, 95.453, 224.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Group IIC Intron ... , 2 types, 2 molecules AB

#1: RNA chain Group IIC Intron Ribozyme


Mass: 126651.008 Da / Num. of mol.: 1 / Fragment: domains 1-5 / Mutation: C289G/C358G/G385C / Source method: obtained synthetically / Details: in vitro transcription system / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#2: RNA chain Group IIC Intron Ribozyme


Mass: 2583.569 Da / Num. of mol.: 1 / Fragment: 5'-exon / Source method: obtained synthetically / Details: in vitro transcription system / Source: (synth.) Oceanobacillus iheyensis (bacteria)

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Non-polymers , 5 types, 88 molecules

#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.68 Å3/Da / Density % sol: 66.6 % / Mosaicity: 0.19 °
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 potassium chloride, 10 mM lithium 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: 3.44→48.46 Å / Num. obs: 24334 / % possible obs: 94.1 % / Redundancy: 3.3 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.081 / Rsym value: 0.053 / Net I/av σ(I): 9.7 / Net I/σ(I): 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRsym value% possible allRrim(I) all
3.44-3.633.21.5080.435280.8621.50895
3.63-3.8530.6411.130750.4590.64187.50.802
3.85-4.113.20.3042.329460.2370.30488.90.422
4.11-4.443.40.1415.430740.0970.14198.70.186
4.44-4.873.30.0781027940.0550.07897.30.103
4.87-5.443.40.04716.224950.0340.04795.40.065
5.44-6.283.40.03323.222850.0250.03398.60.047
6.28-7.693.20.02429.418570.0210.02494.90.039
7.69-10.883.40.01641.115050.0120.01696.90.023
10.88-48.4583.20.01530.67750.0110.01587.30.021

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Processing

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

4far


Resolution: 3.44→48.46 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 70.519 / SU ML: 0.497 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.582
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 1201 5.1 %RANDOM
Rwork0.2092 ---
obs0.2117 22183 89.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 381.33 Å2 / Biso mean: 128.376 Å2 / Biso min: 36.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å2-0 Å2-0 Å2
2---2.94 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 3.44→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8478 101 38 8617
Biso mean--87.43 67.54 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0119552
X-RAY DIFFRACTIONr_bond_other_d0.0030.023924
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.28114877
X-RAY DIFFRACTIONr_angle_other_deg1.67739526
X-RAY DIFFRACTIONr_chiral_restr0.1180.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024788
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022130
LS refinement shellResolution: 3.441→3.529 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.596 80 -
Rwork0.563 1491 -
all-1571 -
obs--83.12 %
Refinement TLS params.Method: refined / Origin x: 23.848 Å / Origin y: 9.124 Å / Origin z: 475.56 Å
111213212223313233
T0.3585 Å2-0.0463 Å20.0469 Å2-0.2741 Å20.0653 Å2--0.2319 Å2
L0.6536 °2-0.9155 °2-0.7453 °2-2.7145 °21.0415 °2--1.7158 °2
S-0.1941 Å °-0.265 Å °-0.1528 Å °0.7427 Å °0.1074 Å °0.1763 Å °0.2599 Å °0.1096 Å °0.0866 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 390
2X-RAY DIFFRACTION1B-4 - 0

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