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- PDB-8vax: Cadmium catalyzed primer extension product with 14mer primer and ... -

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Basic information

Entry
Database: PDB / ID: 8vax
TitleCadmium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer
ComponentsCadmium catalyzed nonenzymatic RNA primer extension product
KeywordsRNA / Phosphorothioate / Cadmium / thiophilic 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: 1.417 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Cadmium catalyzed nonenzymatic RNA primer extension product
BBB: Cadmium catalyzed nonenzymatic RNA primer extension product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5649
Polymers9,7482
Non-polymers8167
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.471, 43.471, 83.887
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
11BBB-105-

MG

21AAA-217-

HOH

31AAA-234-

HOH

41BBB-205-

HOH

51BBB-281-

HOH

61BBB-282-

HOH

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Components

#1: RNA chain Cadmium 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.: 5 / 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.: 183 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 35% w/v 1,6-Hexanediol, 50 mM TRIS pH 8.5 75 mM Magnesium sulfate.

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.03579 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03579 Å / Relative weight: 1
ReflectionResolution: 1.417→50 Å / Num. obs: 16509 / % possible obs: 91.5 % / Redundancy: 7.2 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.035 / Rrim(I) all: 0.101 / Χ2: 0.953 / Net I/σ(I): 19.6
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 502 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.198 / Rrim(I) all: 0.35 / Χ2: 0.661 / % possible all: 56.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.417→41.944 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.207 / SU B: 1.006 / SU ML: 0.041 / Average fsc free: 0.9699 / Average fsc work: 0.9793 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.218 841 5.146 %
Rwork0.1749 15502 -
all0.177 --
obs-16343 90.188 %
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: 12.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0.001 Å2-0 Å2
2---0.001 Å20 Å2
3---0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.417→41.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 644 51 183 878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.017774
X-RAY DIFFRACTIONr_bond_other_d0.0290.023348
X-RAY DIFFRACTIONr_angle_refined_deg2.8682.2961178
X-RAY DIFFRACTIONr_angle_other_deg3.7632.467822
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.057514
X-RAY DIFFRACTIONr_chiral_restr0.1350.2152
X-RAY DIFFRACTIONr_chiral_restr_other1.7860.224
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.021400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023128
X-RAY DIFFRACTIONr_nbd_refined0.0840.271
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.2443
X-RAY DIFFRACTIONr_nbtor_refined0.2510.2307
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.2640.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3330.2183
X-RAY DIFFRACTIONr_metal_ion_refined0.0360.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.213
X-RAY DIFFRACTIONr_nbd_other0.1820.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.231
X-RAY DIFFRACTIONr_scbond_it2.5861.525774
X-RAY DIFFRACTIONr_scbond_other2.3171.481770
X-RAY DIFFRACTIONr_scangle_it4.1892.761178
X-RAY DIFFRACTIONr_scangle_other4.0172.6911173
X-RAY DIFFRACTIONr_lrange_it5.68918.7281215
X-RAY DIFFRACTIONr_lrange_other5.48817.631118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.417-1.4540.19360.1966170.19613470.980.97348.47810.186
1.454-1.4940.215360.217950.2112680.9690.9765.53630.201
1.494-1.5370.206380.1938770.19412270.9720.97574.57210.185
1.537-1.5840.252450.2019700.20312120.9620.97483.74590.197
1.584-1.6360.231580.18310300.18611760.9670.97892.5170.182
1.636-1.6940.205500.16310670.16511270.9740.98399.11270.166
1.694-1.7570.235500.15710520.1611100.9680.98499.27930.166
1.757-1.8290.171480.16210090.16310590.9820.98399.81110.172
1.829-1.910.22760.1699370.17310160.9660.98199.70470.183
1.91-2.0030.19400.1759380.1769800.9730.9899.79590.191
2.003-2.1110.202410.1798760.189190.9760.98199.78240.209
2.111-2.2390.192520.1698440.1718960.9770.9811000.196
2.239-2.3930.234500.187880.1838400.9610.9899.76190.215
2.393-2.5840.252300.1817550.1847850.9750.981000.226
2.584-2.830.254430.1946720.1977170.9650.97699.72110.237
2.83-3.1620.308450.1896180.1966700.9540.97998.95520.239
3.162-3.6480.258390.1715480.1755920.9580.98499.15540.231
3.648-4.4590.131290.1334720.1335040.990.98999.40480.194
4.459-6.2710.203210.1543950.1564160.9760.9871000.242
6.271-41.9440.195140.2432420.2412590.9690.95198.84170.442

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