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- PDB-5y85: Structure-based Insights into Self-Cleavage by a Four-way Junctio... -

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Entry
Database: PDB / ID: 5y85
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
Specimen sourcemetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.001 Å resolution
AuthorsZheng, L. / Micura, R.L. / Ren, A.
Funding supportChina , 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China91640104China
National Natural Science Foundation of China31670826China
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 18, 2017 / Release: Nov 22, 2017

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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)44,37630
Polyers43,7444
Non-polymers63226
Water2,936163
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)22,18815
Polyers21,8722
Non-polymers31613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3700
ΔGint (kcal/M)-94
Surface area (Å2)11350
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)22,18815
Polyers21,8722
Non-polymers31613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3740
ΔGint (kcal/M)-98
Surface area (Å2)11260
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)91.182, 109.304, 41.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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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: (synth.) metagenome (others)
#2: DNA/RNA hybrid DNA/RNA (50-MER)


Mass: 16087.562 Da / Num. of mol.: 2 / Source: (synth.) metagenome (others)
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 26 / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Formula: H2O / Water

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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: 2.38 / Density percent sol: 48.26 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M NaOAc, pH 5.2, 0.15M CaCl2, 18-22% iso-propanol or MPD

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Collection date: Jan 1, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionD resolution high: 2 Å / D resolution low: 50 Å / Number obs: 28779 / NetI over sigmaI: 16.4 / Redundancy: 4.4 % / Percent possible obs: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.36 / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 36.2
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Least-squares processR factor R free: 0.2374 / R factor R work: 0.2178 / R factor obs: 0.2189 / Highest resolution: 2.001 Å / Lowest resolution: 35.852 Å / Number reflection R free: 1442 / Number reflection obs: 28779 / Percent reflection R free: 5.01 / Percent reflection obs: 99.37
Refine hist #LASTHighest resolution: 2.001 Å / Lowest resolution: 35.852 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 2904 / Ligand: 26 / Solvent: 163 / Total: 3093
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183382
X-RAY DIFFRACTIONf_angle_d0.4005044
X-RAY DIFFRACTIONf_dihedral_angle_d10.8451616
X-RAY DIFFRACTIONf_chiral_restr0.022678
X-RAY DIFFRACTIONf_plane_restr0.002136
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.00110.40130.34742.0726117266998.00
2.07260.37260.32982.15551232703100.00
2.15550.43860.36202.2536140268699.00
2.25360.41110.31912.3724151269499.00
2.37240.37430.30002.52101572693100.00
2.52100.35370.29792.71561502724100.00
2.71560.29810.28482.98881402739100.00
2.98880.24670.21533.42101622738100.00
3.42100.21980.18474.3089150277399.00
4.30890.15960.169035.8579152291899.00

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