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- PDB-8ydc: Crystal structure of a hammerhead ribozyme with pseudoknot -

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Basic information

Entry
Database: PDB / ID: 8ydc
TitleCrystal structure of a hammerhead ribozyme with pseudoknot
Components
  • DNA/RNA (5'-R(*AP*CP*AP*UP*GP*UP*CP*U)-D(P*C)-R(P*UP*GP*GP*GP*A)-3')
  • ribozyme strand
KeywordsRNA / catalysis
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 Å
AuthorsLiu, Y. / Zhan, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)82111530210 China
National Science Foundation (NSF, China)21877065 China
CitationJournal: Nat Commun / Year: 2024
Title: The structure and catalytic mechanism of a pseudoknot-containing hammerhead ribozyme.
Authors: Zhan, X. / Wilson, T.J. / Li, Z. / Zhang, J. / Yang, Y. / Lilley, D.M.J. / Liu, Y.
History
DepositionFeb 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,6863
Polymers23,1632
Non-polymers5231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.578, 83.578, 258.790
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 ribozyme strand


Mass: 18715.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (code 3) (others)
#2: DNA/RNA hybrid DNA/RNA (5'-R(*AP*CP*AP*UP*GP*UP*CP*U)-D(P*C)-R(P*UP*GP*GP*GP*A)-3')


Mass: 4447.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestY

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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: 5.51 Å3/Da / Density % sol: 77.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Magnesium acetate tetrahydrate MES monohydrate Ammonium sulfate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.89→16.25 Å / Num. obs: 12665 / % possible obs: 98.38 % / Redundancy: 37.8 % / CC1/2: 1 / Net I/σ(I): 18.05
Reflection shellResolution: 2.89→2.993 Å / Num. unique obs: 1226 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.89→16.25 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 642 5.11 %
Rwork0.1954 --
obs0.196 12565 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→16.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1549 0 0 1549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.866
X-RAY DIFFRACTIONf_dihedral_angle_d16.742857
X-RAY DIFFRACTIONf_chiral_restr0.076356
X-RAY DIFFRACTIONf_plane_restr0.01172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.110.40011170.37422304X-RAY DIFFRACTION99
3.11-3.420.29231420.24582295X-RAY DIFFRACTION99
3.42-3.910.25511310.22822343X-RAY DIFFRACTION99
3.91-4.910.15911232407X-RAY DIFFRACTION99

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