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- PDB-5t5a: Crystal Structure of the Twister Sister (TS) Ribozyme at 2.0 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5t5a
TitleCrystal Structure of the Twister Sister (TS) Ribozyme at 2.0 Angstrom
ComponentsDNA/RNA (71-MER)
KeywordsRNA / RNA junction catalysis
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLilley, D.M.J. / Liu, Y. / Wilson, T.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: The structure of a nucleolytic ribozyme that employs a catalytic metal ion.
Authors: Liu, Y. / Wilson, T.J. / Lilley, D.M.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3May 8, 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_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,35510
Polymers20,1371
Non-polymers2199
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-63 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.304, 39.304, 228.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA/RNA hybrid DNA/RNA (71-MER)


Mass: 20136.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) metagenome (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Source: (synth.) metagenome (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6 / Details: magnesium acetate sodium cacodylate MPD

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91772 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91772 Å / Relative weight: 1
ReflectionResolution: 2→37.16 Å / Num. all: 12723 / Num. obs: 268378 / % possible obs: 97 % / Redundancy: 21.1 % / Rmerge(I) obs: 0.07359 / Net I/σ(I): 28.95
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.3758 / Num. unique all: 1014

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.10.1_2155: ???)phasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.16 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.88
RfactorNum. reflection% reflection
Rfree0.2171 1081 4.81 %
Rwork0.1698 --
obs0.1721 22488 97.37 %
all-12722 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1320 44 99 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131516
X-RAY DIFFRACTIONf_angle_d1.9872379
X-RAY DIFFRACTIONf_dihedral_angle_d12.335718
X-RAY DIFFRACTIONf_chiral_restr0.09307
X-RAY DIFFRACTIONf_plane_restr0.01862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.09120.2661140.22062273X-RAY DIFFRACTION83
2.0912-2.20150.24251240.20732682X-RAY DIFFRACTION97
2.2015-2.33940.27931440.21482714X-RAY DIFFRACTION100
2.3394-2.51990.271260.21372777X-RAY DIFFRACTION100
2.5199-2.77350.31270.2192760X-RAY DIFFRACTION100
2.7735-3.17460.23541660.19192697X-RAY DIFFRACTION100
3.1746-3.99890.20351420.1382773X-RAY DIFFRACTION100
3.9989-37.17110.14851380.12582731X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.2382 Å / Origin y: 18.6981 Å / Origin z: 85.0628 Å
111213212223313233
T0.1671 Å2-0.0105 Å2-0.0108 Å2-0.2028 Å2-0.0209 Å2--0.2159 Å2
L1.1081 °2-0.0411 °2-0.2341 °2-0.7671 °2-0.2281 °2--0.236 °2
S-0.0337 Å °0.0553 Å °0.0511 Å °0.0263 Å °0.0414 Å °0.019 Å °-0.0337 Å °-0.0744 Å °-0.0106 Å °
Refinement TLS groupSelection details: all

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