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- PDB-6u6j: RNA-monomer complex containing pyrophosphate linkage -

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Basic information

Entry
Database: PDB / ID: 6u6j
TitleRNA-monomer complex containing pyrophosphate linkage
ComponentsRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(DPG))-3')
KeywordsRNA / pyrophosphate
Function / homologyChem-EQ4 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, W. / Szostak, J.W. / Giurgiu, C. / Wright, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Prebiotically Plausible "Patching" of RNA Backbone Cleavage through a 3'-5' Pyrophosphate Linkage.
Authors: Wright, T.H. / Giurgiu, C. / Zhang, W. / Radakovic, A. / O'Flaherty, D.K. / Zhou, L. / Szostak, J.W.
History
DepositionAug 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(DPG))-3')
B: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(DPG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7334
Polymers9,8762
Non-polymers8572
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint15 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.304, 43.304, 84.303
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

21B-205-

HOH

31B-208-

HOH

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Components

#1: RNA chain RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G*(DPG))-3')


Mass: 4937.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-EQ4 / 5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine


Type: RNA linking / Mass: 428.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C13H17N8O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10mM MgCl2, 1.8 M Ammonium citrate tribasic pH 7.0

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 12495 / % possible obs: 98.9 % / Redundancy: 10.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.059 / Χ2: 0.854 / Net I/σ(I): 44.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1234 / CC1/2: 0.991 / Χ2: 0.388

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C8D

6c8d


Resolution: 1.6→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28 630 5.1 %RANDOM
Rwork0.23 ---
obs0.23 11788 98.21 %-
Displacement parametersBiso mean: 27.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 598 112 35 745
LS refinement shellResolution: 1.601→1.642 Å
RfactorNum. reflection% reflection
Rfree0.285 845 -
Rwork0.249 --
obs--97.02 %

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