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- PDB-5dh6: Two divalent metal ions and conformational changes play roles in ... -

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Basic information

Entry
Database: PDB / ID: 5dh6
TitleTwo divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in Mg2+
Components
  • 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'
  • hammerhead ribozyme
KeywordsRNA / ribozyme / hammerhead
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.784 Å
AuthorsMir, A. / Chen, J. / Neau, D. / Golden, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095923 United States
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
DepositionAug 29, 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, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hammerhead ribozyme
B: 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)22,0447
Polymers21,9222
Non-polymers1225
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-37 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.405, 85.964, 102.969
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
11B-202-

HOH

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Components

#1: RNA chain hammerhead ribozyme


Mass: 15484.287 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 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.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 33% MPD, 0.4 M potassium chloride, 50 mM potassium acetate, 10 mM MgCl2, pH 5.0, and 0.5mM spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.784→50 Å / Num. all: 9318 / Num. obs: 9318 / % possible obs: 99.5 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 61.7
Reflection shellResolution: 2.784→2.85 Å / Redundancy: 15 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 6.3 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.784→28.407 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 920 9.97 %
Rwork0.2108 --
obs0.2139 9231 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.784→28.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1454 5 8 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021626
X-RAY DIFFRACTIONf_angle_d0.472532
X-RAY DIFFRACTIONf_dihedral_angle_d10.131807
X-RAY DIFFRACTIONf_chiral_restr0.023338
X-RAY DIFFRACTIONf_plane_restr0.00368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7843-2.9310.36021260.35271141X-RAY DIFFRACTION96
2.931-3.11440.33061340.26071160X-RAY DIFFRACTION98
3.1144-3.35450.23361210.22311158X-RAY DIFFRACTION98
3.3545-3.69150.25851310.20651193X-RAY DIFFRACTION99
3.6915-4.22410.21071370.18711190X-RAY DIFFRACTION100
4.2241-5.31620.20541330.18491196X-RAY DIFFRACTION100
5.3162-28.40860.23731380.20781273X-RAY DIFFRACTION100

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