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- PDB-4ds6: Crystal structure of a group II intron in the pre-catalytic state -

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Basic information

Entry
Database: PDB / ID: 4ds6
TitleCrystal structure of a group II intron in the pre-catalytic state
ComponentsMutant Group IIC Intron
KeywordsRNA / RIBONUCLEIC ACID / INTRON / GROUP II
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.644 Å
AuthorsChan, R.T. / Robart, A.R. / Rajashankar, K.R. / Pyle, A.M. / Toor, N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Crystal structure of a group II intron in the pre-catalytic state.
Authors: Chan, R.T. / Robart, A.R. / Rajashankar, K.R. / Pyle, A.M. / Toor, N.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Sep 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 / struct_conn / struct_site
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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Mutant Group IIC Intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,28917
Polymers136,9001
Non-polymers38916
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.880, 95.310, 226.173
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 Mutant Group IIC Intron


Mass: 136900.062 Da / Num. of mol.: 1 / Mutation: G359A / Source method: isolated from a natural source / Source: (natural) Oceanobacillus iheyensis (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.54 Å3/Da / Density % sol: 65.24 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5mM spermine, 10mM magnesium acetate, 50mM MES pH 5.6, 2.3M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2011
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.644→40.406 Å / Num. all: 22036 / Num. obs: 22036 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IGI

3igi


Resolution: 3.644→40.406 Å / SU ML: 0.44 / σ(F): 1.33 / Phase error: 25.98 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2485 1973 8.95 %
Rwork0.205 --
obs0.205 22036 98.36 %
all-24009 -
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 126.89 Å2 / ksol: 0.271 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8939 Å2-0 Å20 Å2
2---10.7746 Å2-0 Å2
3---13.6685 Å2
Refinement stepCycle: LAST / Resolution: 3.644→40.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8429 16 29 8474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089445
X-RAY DIFFRACTIONf_angle_d0.98314733
X-RAY DIFFRACTIONf_dihedral_angle_d20.9334711
X-RAY DIFFRACTIONf_chiral_restr0.0631963
X-RAY DIFFRACTIONf_plane_restr0.006391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6441-3.73520.44161190.40951326X-RAY DIFFRACTION92
3.7352-3.83610.3011480.27681380X-RAY DIFFRACTION97
3.8361-3.94890.3811310.31611383X-RAY DIFFRACTION97
3.9489-4.07620.28161530.2421396X-RAY DIFFRACTION98
4.0762-4.22180.24861300.22331436X-RAY DIFFRACTION99
4.2218-4.39060.29141460.21211425X-RAY DIFFRACTION100
4.3906-4.59020.25161370.21661432X-RAY DIFFRACTION99
4.5902-4.83180.28251320.22141454X-RAY DIFFRACTION99
4.8318-5.13390.2561430.20071424X-RAY DIFFRACTION100
5.1339-5.52940.23271430.19481454X-RAY DIFFRACTION100
5.5294-6.08420.22561520.17681463X-RAY DIFFRACTION100
6.0842-6.96070.22991420.181468X-RAY DIFFRACTION100
6.9607-8.75510.20571500.16191502X-RAY DIFFRACTION100
8.7551-40.40840.22361470.18781520X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -24.879 Å / Origin y: 7.8453 Å / Origin z: -25.7753 Å
111213212223313233
T0.9661 Å2-0.0639 Å20.0746 Å2-1.014 Å20.0658 Å2--0.9184 Å2
L0.0374 °20.0017 °20.0205 °2-0.4019 °20.0428 °2--0.1759 °2
S-0.0939 Å °0.2705 Å °0.013 Å °-0.3662 Å °0.1306 Å °-0.1741 Å °0.0266 Å °0.072 Å °-0.0087 Å °
Refinement TLS groupSelection details: all

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