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- PDB-8vaw: Magnesium catalyzed primer extension product with 14mer primer an... -

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Basic information

Entry
Database: PDB / ID: 8vaw
TitleMagnesium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer
ComponentsMagnesium catalyzed nonenzymatic RNA primer extension product
KeywordsRNA / Phosphorothioate / Magnesium / oxophilic metal ion / nonenzymatic primer extension
Function / homology2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsFang, Z. / Szostak, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 2104708 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.
Authors: Fang, Z. / Pazienza, L.T. / Zhang, J. / Tam, C.P. / Szostak, J.W.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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 2.0Jul 30, 2025Group: Atomic model / Structure summary / Category: atom_site / pdbx_entry_details
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnesium catalyzed nonenzymatic RNA primer extension product
B: Magnesium catalyzed nonenzymatic RNA primer extension product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5408
Polymers9,7482
Non-polymers7926
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.570, 43.570, 84.342
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-202-

MG

21B-202-

MG

31A-336-

HOH

41A-341-

HOH

51A-375-

HOH

61B-305-

HOH

71B-321-

HOH

81B-383-

HOH

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Components

#1: RNA chain Magnesium catalyzed nonenzymatic RNA primer extension product


Mass: 4874.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.5 M Sodium chloride, 50 mM TRIS pH 7.5, 0.25 M Magnesium chloride.

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 27390 / % possible obs: 98.4 % / Redundancy: 8.4 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.014 / Rrim(I) all: 0.042 / Χ2: 0.889 / Net I/σ(I): 50.2
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 968 / CC1/2: 0.842 / CC star: 0.956 / Rpim(I) all: 0.255 / Rrim(I) all: 0.499 / Χ2: 1.13 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→37.733 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.688 / SU ML: 0.03 / Cross valid method: NONE / ESU R: 0.05 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1908 1156 4.654 %
Rwork0.1878 23685 -
all0.188 --
obs-24841 94.034 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.775 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20 Å20 Å2
2--0.001 Å2-0 Å2
3----0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.25→37.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 690 4 165 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.016774
X-RAY DIFFRACTIONr_bond_other_d0.0280.023348
X-RAY DIFFRACTIONr_angle_refined_deg2.9262.2061178
X-RAY DIFFRACTIONr_angle_other_deg3.4682.34822
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.079516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2152
X-RAY DIFFRACTIONr_chiral_restr_other1.6930.220
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.021400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022128
X-RAY DIFFRACTIONr_nbd_refined0.1890.284
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.2440
X-RAY DIFFRACTIONr_nbtor_refined0.2470.2307
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.2650.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2730.2116
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.225
X-RAY DIFFRACTIONr_nbd_other0.1670.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.234
X-RAY DIFFRACTIONr_scbond_it2.9351.653774
X-RAY DIFFRACTIONr_scbond_other2.9341.653774
X-RAY DIFFRACTIONr_scangle_it3.7532.981178
X-RAY DIFFRACTIONr_scangle_other3.7522.981179
X-RAY DIFFRACTIONr_lrange_it5.49520.7821159
X-RAY DIFFRACTIONr_lrange_other5.1620.4211098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.28410.256702X-RAY DIFFRACTION38.1809
1.282-1.3180.287730.2321478X-RAY DIFFRACTION82.5
1.318-1.3560.189711686X-RAY DIFFRACTION98.7634
1.356-1.3970.222790.2081699X-RAY DIFFRACTION100
1.397-1.4430.211740.1911636X-RAY DIFFRACTION99.9416
1.443-1.4940.226840.1911549X-RAY DIFFRACTION100
1.494-1.550.199640.1851565X-RAY DIFFRACTION100
1.55-1.6130.191711489X-RAY DIFFRACTION100
1.613-1.6850.247690.1841405X-RAY DIFFRACTION99.9322
1.685-1.7670.205660.1831359X-RAY DIFFRACTION100
1.767-1.8620.206630.1821296X-RAY DIFFRACTION100
1.862-1.9750.18570.1791227X-RAY DIFFRACTION99.8445
1.975-2.1110.159621166X-RAY DIFFRACTION99.9186
2.111-2.2790.208410.1881103X-RAY DIFFRACTION100
2.279-2.4960.239580.186990X-RAY DIFFRACTION99.9047
2.496-2.7890.194570.219910X-RAY DIFFRACTION100
2.789-3.2170.239390.191807X-RAY DIFFRACTION99.2958
3.217-3.9330.13936708X-RAY DIFFRACTION99.2
3.933-5.5330.13635557X-RAY DIFFRACTION100
5.533-37.7330.1916352X-RAY DIFFRACTION99.4595

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