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- PDB-4rgf: Crystal structure of the in-line aligned env22 twister ribozyme s... -

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Basic information

Entry
Database: PDB / ID: 4rgf
TitleCrystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+
Componentsenv22 twister ribozyme
KeywordsRNA / pseudoknot / stems / cleavage
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciesSynthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2008 Å
AuthorsRen, A. / Rajashankar, K.R. / Simanshu, D. / Patel, D.
CitationJournal: Nat Commun / Year: 2014
Title: In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.
Authors: Ren, A. / Kosutic, M. / Rajashankar, K.R. / Frener, M. / Santner, T. / Westhof, E. / Micura, R. / Patel, D.J.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 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_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_asym_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_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: env22 twister ribozyme
B: env22 twister ribozyme
C: env22 twister ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,20829
Polymers54,0323
Non-polymers1,17626
Water724
1
A: env22 twister ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,55913
Polymers18,0111
Non-polymers54812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: env22 twister ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3168
Polymers18,0111
Non-polymers3057
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: env22 twister ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3338
Polymers18,0111
Non-polymers3227
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.299, 64.299, 584.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain env22 twister ribozyme


Mass: 18010.756 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Synthetic (others)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.1 M imidole, pH 7.9, CaCl2 0.2 M, 20% PEG1000,50 mM MnCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→48.75 Å / Num. all: 22031 / Num. obs: 21084 / % possible obs: 95.7 % / Observed criterion σ(F): 0.7 / Observed criterion σ(I): 0.7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 0.7 / Rsym value: 0.436 / % possible all: 71.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2008→48.749 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 1020 4.84 %
Rwork0.2314 --
obs0.2335 21084 94.57 %
all-22031 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2008→48.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3541 26 4 3571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083961
X-RAY DIFFRACTIONf_angle_d1.1366161
X-RAY DIFFRACTIONf_dihedral_angle_d17.9151976
X-RAY DIFFRACTIONf_chiral_restr0.06820
X-RAY DIFFRACTIONf_plane_restr0.006167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2008-3.36950.38611040.3222072X-RAY DIFFRACTION68
3.3695-3.58060.35361500.30932874X-RAY DIFFRACTION95
3.5806-3.85690.28491460.27353009X-RAY DIFFRACTION100
3.8569-4.24480.27241630.22373030X-RAY DIFFRACTION100
4.2448-4.85860.25561690.21723008X-RAY DIFFRACTION100
4.8586-6.11940.2611320.22383043X-RAY DIFFRACTION100
6.1194-48.75490.26951560.21363028X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.3258 Å / Origin y: -11.2203 Å / Origin z: 17.5405 Å
111213212223313233
T1.1885 Å2-0.1294 Å2-0.0922 Å2-1.7623 Å20.4874 Å2--1.1831 Å2
L0.6714 °2-0.5401 °2-0.4787 °2-1.6097 °20.7951 °2--0.7616 °2
S0.003 Å °-0.3101 Å °0.0561 Å °0.4453 Å °0.0093 Å °-0.2422 Å °-0.0889 Å °0.1728 Å °0.0173 Å °
Refinement TLS groupSelection details: all

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