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- PDB-3bwp: Crystal structure of a self-spliced group II intron -

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Basic information

Entry
Database: PDB / ID: 3bwp
TitleCrystal structure of a self-spliced group II intron
ComponentsGroup IIC intron
KeywordsRNA / Ribonucleic acid / Intron / Group II
Function / homology: / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsToor, N. / Keating, K.S. / Taylor, S.D. / Pyle, A.M.
CitationJournal: Science / Year: 2008
Title: Crystal structure of a self-spliced group II intron
Authors: Toor, N. / Keating, K.S. / Taylor, S.D. / Pyle, A.M.
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jun 6, 2018Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)133,90010
Polymers133,6521
Non-polymers2489
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.854, 94.958, 225.910
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: 133652.156 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence occurs naturally in Oceanobacillus iheyensis. Sequence modified using PCR
References: GenBank: 42632302
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 6% PEG 3350, 150 mM magnesium acetate, 350 mM KCl, 50 mM Na-HEPES pH 7.0, 0.5 mM spermine, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2magnesium acetate11
3KCl11
4Na-HEPES11
5PEG 335012
6magnesium acetate12
7KCl12
8Na-HEPES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2007
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 34541 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Rmerge(I) obs: 0.149 / Χ2: 0.988 / Net I/σ(I): 12.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3365 / Χ2: 1.023 / % possible all: 98.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHELXmodel building
CNS1.2refinement
PDB_EXTRACT3.004data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: Parkinson, Vojtechovsky, Clowney, Brunger & Berman
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1674 -random
Rwork0.2762 ---
all-35502 --
obs-33356 94 %-
Displacement parametersBiso mean: 79.413 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 7592 9 8 7609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_improper_angle_d1.63
LS refinement shellResolution: 3.1→3.21 Å
RfactorNum. reflection% reflection
Rfree0.2878 96 -
Rwork0.2889 --
obs-2314 98.7 %

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