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- PDB-4e8r: Structure of Oceanobacillus iheyensis group II intron in a ligand... -

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Basic information

Entry
Database: PDB / ID: 4e8r
TitleStructure of Oceanobacillus iheyensis group II intron in a ligand-free state in the presence of Cs+ and Mg2+
ComponentsGroup IIC intron
KeywordsRNA / ribozyme / metalloenzyme / self-splicing / retrotransposition
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 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_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_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_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_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_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

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Assembly

Deposited unit
A: Group IIC intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,04964
Polymers127,6471
Non-polymers6,40263
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.200, 94.915, 225.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24.305 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Cs
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


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


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM magnesium acetate, 200 mM cesium chloride, 50 mM HEPES sodium, pH 7.0, 4% 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: 1.4861 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4861 Å / Relative weight: 1
ReflectionResolution: 3.36→48.503 Å / Num. obs: 26102 / % possible obs: 97.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.1
Reflection shellResolution: 3.36→3.45 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2 / % possible all: 96.8

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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: 3.36→48.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 43.209 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25799 1384 5 %RANDOM
Rwork0.20035 ---
obs0.20325 26102 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 134.279 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å20 Å20 Å2
2--0.43 Å20 Å2
3----3.46 Å2
Refinement stepCycle: LAST / Resolution: 3.36→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8412 122 26 8560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0119490
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3921.47514788
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_restr0.1590.21578
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024099
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: 3.364→3.451 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 87 -
Rwork0.29 1741 -
obs--95.66 %
Refinement TLS params.Method: refined / Origin x: -24.889 Å / Origin y: 8.207 Å / Origin z: -25.363 Å
111213212223313233
T0.4173 Å2-0.0326 Å20.0463 Å2-0.4201 Å2-0.0315 Å2--0.4213 Å2
L0.5275 °20.6117 °2-0.7175 °2-1.4006 °2-0.8556 °2--1.0669 °2
S-0.1468 Å °0.2176 Å °-0.1576 Å °-0.5031 Å °0.0512 Å °-0.1446 Å °0.1314 Å °-0.1954 Å °0.0956 Å °

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