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- PDB-5y87: Structure-based Insights into Self-Cleavage by a Four-way Junctio... -

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Basic information

Entry
Database: PDB / ID: 5y87
TitleStructure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister Ribozyme
Components
  • DNA/RNA (50-MER)
  • RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3')
KeywordsRNA / twister-sister / Riboyzme / Catalysis / self-cleaving / Mn2+ soaking
Function / homology: / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.132 Å
AuthorsZheng, L. / Micura, R.L. / Ren, A.
CitationJournal: Nat Commun / Year: 2017
Title: Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme
Authors: Zheng, L. / Mairhofer, E. / Teplova, M. / Zhang, Y. / Ma, J. / Patel, D.J. / Micura, R. / Ren, A.
History
DepositionAug 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1Mar 27, 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
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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3')
B: DNA/RNA (50-MER)
C: RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3')
D: DNA/RNA (50-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,95326
Polymers43,7444
Non-polymers1,20922
Water5,152286
1
A: RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3')
B: DNA/RNA (50-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,58615
Polymers21,8722
Non-polymers71413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-79 kcal/mol
Surface area10870 Å2
MethodPISA
2
C: RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3')
D: DNA/RNA (50-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,36711
Polymers21,8722
Non-polymers4949
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-71 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.221, 108.963, 41.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain RNA (5'-R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3')


Mass: 5784.555 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) metagenome (others)
#2: DNA/RNA hybrid DNA/RNA (50-MER)


Mass: 16087.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) metagenome (others)
#3: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M NaOAc, pH 5.2, 0.15M CaCl2, 18-22% MPD, 50-100mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.65 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 44790 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 23.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.132→42.073 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.95
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2571 2316 5.17 %
Rwork0.2022 --
obs0.2051 44790 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.132→42.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2904 22 286 3212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053240
X-RAY DIFFRACTIONf_angle_d1.0065044
X-RAY DIFFRACTIONf_dihedral_angle_d11.4491616
X-RAY DIFFRACTIONf_chiral_restr0.042678
X-RAY DIFFRACTIONf_plane_restr0.006136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1325-2.1760.37781370.32062491X-RAY DIFFRACTION98
2.176-2.22330.36551260.29352476X-RAY DIFFRACTION100
2.2233-2.2750.33951390.27512480X-RAY DIFFRACTION100
2.275-2.33190.27891310.25952575X-RAY DIFFRACTION100
2.3319-2.3950.3521420.25562427X-RAY DIFFRACTION100
2.395-2.46540.36111300.25212551X-RAY DIFFRACTION100
2.4654-2.5450.34231190.25752487X-RAY DIFFRACTION100
2.545-2.6360.42261520.27492517X-RAY DIFFRACTION100
2.636-2.74150.34431360.28152468X-RAY DIFFRACTION100
2.7415-2.86620.31271430.23992493X-RAY DIFFRACTION100
2.8662-3.01730.30011190.23162535X-RAY DIFFRACTION100
3.0173-3.20630.27461400.21212489X-RAY DIFFRACTION100
3.2063-3.45370.25581310.19142523X-RAY DIFFRACTION100
3.4537-3.80110.20271750.17832467X-RAY DIFFRACTION100
3.8011-4.35060.21181410.14692469X-RAY DIFFRACTION100
4.3506-5.47940.19341310.13752511X-RAY DIFFRACTION100
5.4794-42.08140.18791240.17562515X-RAY DIFFRACTION100

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