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- PDB-4qjh: Crystal Structure of the Twister Ribozyme with the Nucleotide 5'-... -

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Basic information

Entry
Database: PDB / ID: 4qjh
TitleCrystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution
Components(Twister Ribozyme) x 2
KeywordsRNA / small self-cleaving ribozyme
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.88 Å
AuthorsEiler, D.R. / Wang, J. / Steitz, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme.
Authors: Eiler, D. / Wang, J. / Steitz, T.A.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_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: Twister Ribozyme
B: Twister Ribozyme
C: Twister Ribozyme
D: Twister Ribozyme
E: Twister Ribozyme
F: Twister Ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,04110
Polymers71,9446
Non-polymers974
Water1086
1
A: Twister Ribozyme
B: Twister Ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0063
Polymers23,9812
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-5 kcal/mol
Surface area12040 Å2
MethodPISA
2
C: Twister Ribozyme
D: Twister Ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0545
Polymers23,9812
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-25 kcal/mol
Surface area12160 Å2
MethodPISA
3
E: Twister Ribozyme
F: Twister Ribozyme


Theoretical massNumber of molelcules
Total (without water)23,9812
Polymers23,9812
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-8 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.770, 228.770, 101.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-101-

MG

21E-101-

HOH

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Components

#1: RNA chain Twister Ribozyme


Mass: 8257.906 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: RNA chain Twister Ribozyme


Mass: 15723.355 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase.
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3

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Sample preparation

CrystalDensity Matthews: 5.31 Å3/Da / Density % sol: 76.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 160 mM sodium citrate, pH 4.6, 700 mM ammonium sulfate, 1 M lithium sulfate, 3% pentaerythriotol ethoxylate (3/4 EO/OH), 3% 6-aminohexanoic acid, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.1051
SYNCHROTRONAPS 24-ID-C21.8456
SYNCHROTRONAPS 24-ID-C31.8445
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELFeb 21, 2014
DECTRIS PILATUS 6M-F2PIXELFeb 21, 2014
DECTRIS PILATUS 6M-F3PIXELFeb 20, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1cryo-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2cryo-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
3cryo-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.10511
21.84561
31.84451
ReflectionResolution: 2.018→198.121 Å / Num. all: 99843 / Num. obs: 12154 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 20.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
4.1-4.2640.73.8521,2,3100
4.26-4.381,2,3100
4.38-4.521,2,3100
4.52-4.671,2,3100
4.67-4.831,2,3100
4.83-501,2,399.9

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Processing

Software
NameVersionClassification
XDSdata scaling
HKL2Mapmodel building
REFMAC5.8.0073refinement
XDSdata reduction
HKL2Mapphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.88→198.12 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 40.977 / SU ML: 0.512 / Cross valid method: THROUGHOUT / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23224 600 4 %RANDOM
Rwork0.18525 ---
obs0.1873 14227 99.4 %-
all-14918 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 146.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0.42 Å2-0 Å2
2---0.85 Å2-0 Å2
3---2.75 Å2
Refinement stepCycle: LAST / Resolution: 3.88→198.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4764 4 6 4774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0115332
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.3138295
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_restr0.1130.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022307
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.214.6825328
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined20.01610670
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.88→3.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.373 993 -
obs--92.98 %

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