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- PDB-5dqk: Two divalent metal ions and conformational changes play roles in ... -

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Basic information

Entry
Database: PDB / ID: 5dqk
TitleTwo divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mg2+
Components
  • RNA (48-MER)
  • RNA (5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3')
KeywordsRNA / ribozyme / hammerhead
Function / homology: / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.707 Å
AuthorsMir, A. / Chen, J. / Neau, D. / Golden, B.L.
CitationJournal: Biochemistry / Year: 2015
Title: Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.
Authors: Mir, A. / Chen, J. / Robinson, K. / Lendy, E. / Goodman, J. / Neau, D. / Golden, B.L.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.ptnr2_symmetry / _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 / _pdbx_struct_oper_list.symmetry_operation / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (48-MER)
B: RNA (5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1197
Polymers21,9382
Non-polymers1815
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-21 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.764, 86.070, 103.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

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Components

#1: RNA chain RNA (48-MER)


Mass: 15500.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This RNA was made by in vitro transcription / Source: (synth.) synthetic construct (others)
#2: DNA/RNA hybrid RNA (5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3')


Mass: 6437.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized oligonucleotide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 33% MPD, 0.4 M potassium chloride, 50 mM potassium acetate pH 5.0, 10 mM MgCl2 and 0.5mM spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→42 Å / Num. all: 9951 / Num. obs: 9951 / % possible obs: 99.7 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 28
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZD5

3zd5


Resolution: 2.707→26.069 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.19 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2778 968 10.06 %
Rwork0.2242 --
obs0.2296 9627 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.707→26.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1455 5 31 1491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081627
X-RAY DIFFRACTIONf_angle_d1.3782534
X-RAY DIFFRACTIONf_dihedral_angle_d11.539807
X-RAY DIFFRACTIONf_chiral_restr0.046338
X-RAY DIFFRACTIONf_plane_restr0.00968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7065-2.84910.42271210.36141062X-RAY DIFFRACTION85
2.8491-3.02730.35681330.29221186X-RAY DIFFRACTION94
3.0273-3.26070.28361470.21731257X-RAY DIFFRACTION99
3.2607-3.5880.28981360.21621258X-RAY DIFFRACTION99
3.588-4.10550.27831330.20221283X-RAY DIFFRACTION99
4.1055-5.16590.23041480.19291290X-RAY DIFFRACTION100
5.1659-26.06990.2311500.2051323X-RAY DIFFRACTION98

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