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- PDB-4rge: Crystal structure of the in-line aligned env22 twister ribozyme -

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Basic information

Entry
Database: PDB / ID: 4rge
TitleCrystal structure of the in-line aligned env22 twister ribozyme
Componentsenv22 twister ribozyme
KeywordsRNA / pseudoknot / stem / cleavage / deoxyuridine monophosphate
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSynthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

Downloads & links

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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)54,68930
Polymers54,0323
Non-polymers65627
Water1,49583
1
A: env22 twister ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,25411
Polymers18,0111
Non-polymers24310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: env22 twister ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2059
Polymers18,0111
Non-polymers1948
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: env22 twister ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,23010
Polymers18,0111
Non-polymers2199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.071, 64.071, 578.773
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.1 M imidole, pH 7.9, CaCl2 0.2 M and 14-16% PEG1000, 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: 2.8895→55.5 Å / Num. all: 17208 / Num. obs: 17191 / % possible obs: 99.9 % / Observed criterion σ(F): 1.2 / Observed criterion σ(I): 1.2

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXSphasing
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.89→55.487 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 868 5.05 %
Rwork0.1774 --
obs0.1796 17191 99.63 %
all-17208 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→55.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3541 27 83 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063958
X-RAY DIFFRACTIONf_angle_d1.3356161
X-RAY DIFFRACTIONf_dihedral_angle_d16.7411976
X-RAY DIFFRACTIONf_chiral_restr0.059820
X-RAY DIFFRACTIONf_plane_restr0.008167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8895-3.07060.37551630.33212563X-RAY DIFFRACTION98
3.0706-3.30760.25931480.20112600X-RAY DIFFRACTION100
3.3076-3.64040.22091300.16582664X-RAY DIFFRACTION100
3.6404-4.16710.20641330.13472703X-RAY DIFFRACTION100
4.1671-5.24940.19381400.16132774X-RAY DIFFRACTION100
5.2494-55.49730.22141540.18643019X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.94410.1568-0.05881.1419-0.00860.71880.1693-0.2437-0.10770.0443-0.1650.0891-0.03340.3598-0.0060.4116-0.02430.04590.96740.35490.792-18.276-29.25262.3714
22.09240.6677-0.19782.5598-1.43241.1043-0.0554-0.3604-0.09420.0150.27530.31060.7122-0.820.00371.2008-0.1344-0.08161.18010.4110.8311-33.0907-6.351926.6964
31.5464-0.401-0.82040.2625-0.39071.16930.1241-0.60840.12930.1599-0.2307-0.56410.10860.77460.00110.791-0.1651-0.15311.03860.32541.0319-6.11761.99323.8593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:56)
2X-RAY DIFFRACTION2(chain B and resseq 1:56)
3X-RAY DIFFRACTION3(chain C and resseq 1:55)

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