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- PDB-4e8t: Structure of Oceanobacillus iheyensis group II intron in the pres... -

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Basic information

Entry
Database: PDB / ID: 4e8t
TitleStructure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset)
Components
  • 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3'
  • Group IIC intron
KeywordsRNA / ribozyme / metalloenzyme / self-splicing / retrotransposition
Function / homology: / SPERMINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsMarcia, M. / Pyle, A.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Visualizing Group II Intron Catalysis through the Stages of Splicing.
Authors: Marcia, M. / Pyle, A.M.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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(*AP*UP*UP*UP*AP*UP*UP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,50449
Polymers130,1202
Non-polymers3,38447
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-253 kcal/mol
Surface area57380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.458, 95.765, 225.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain Group IIC intron


Mass: 127646.586 Da / Num. of mol.: 1 / Fragment: domains 1-5 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#2: RNA chain 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3'


Mass: 2473.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide

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Non-polymers , 5 types, 87 molecules

#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#6: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM potassium acetate, 100 mM potassium chloride, 100 mM calcium chloride, 50 mM HEPES sodium, pH 7.0, 5% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.6083 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6083 Å / Relative weight: 1
ReflectionResolution: 3.34→48.612 Å / Num. obs: 27121 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.4
Reflection shellResolution: 3.34→3.42 Å / Redundancy: 5 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
ADSCdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IGI

3igi


Resolution: 3.34→48.61 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 39.175 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23544 1444 5.1 %RANDOM
Rwork0.18901 ---
obs0.19129 27121 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 120.704 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2---1.64 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 3.34→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8489 111 40 8640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0119578
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3021.47414913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1310.21587
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.34→3.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 101 -
Rwork0.332 1787 -
obs--99.53 %
Refinement TLS params.Method: refined / Origin x: -25.033 Å / Origin y: 8.801 Å / Origin z: -25.395 Å
111213212223313233
T0.1883 Å20.0612 Å20.0302 Å2-0.1606 Å2-0.0032 Å2--0.188 Å2
L0.8359 °20.9243 °2-0.8535 °2-2.0217 °2-0.9967 °2--1.5347 °2
S-0.1512 Å °0.1961 Å °-0.1466 Å °-0.525 Å °0.08 Å °-0.0819 Å °0.2259 Å °-0.0028 Å °0.0713 Å °

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