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- PDB-7u89: Product of 14mer primer with activated G monomer diastereomer 1 -

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Basic information

Entry
Database: PDB / ID: 7u89
TitleProduct of 14mer primer with activated G monomer diastereomer 1
ComponentsRNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*(G46))-3')
KeywordsRNA / RNA duplex / Phosphorothioate / Non-enzymatic RNA extension
Function / homologyChem-LXI / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFang, Z. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1607034 United States
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
DepositionMar 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*(G46))-3')
B: RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*(G46))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4774
Polymers9,5882
Non-polymers8892
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint19 kcal/mol
Surface area5800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.204, 43.204, 85.638
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-221-

HOH

21A-231-

HOH

31A-238-

HOH

41A-252-

HOH

51B-226-

HOH

61B-234-

HOH

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Components

#1: RNA chain RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*(G46))-3')


Mass: 4794.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-LXI / 5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(sulfanyl)phosphoryl]guanosine


Mass: 444.363 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N8O6PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20 mM Magnesium chloride, 50 mM MOPS pH 7.0, 2.0 M Ammonium sulfate, 0.5 mM Spermine
PH range: 7

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 11662 / % possible obs: 99.6 % / Redundancy: 10.1 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.029 / Rrim(I) all: 0.091 / Net I/σ(I): 21
Reflection shellResolution: 1.65→1.65 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 553 / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.093 / Rrim(I) all: 0.277 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C8O

6c8o


Resolution: 1.65→28.562 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 2.521 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2816 542 5.294 %
Rwork0.216 9696 -
all0.22 --
obs-10238 87.437 %
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: 15.201 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0.001 Å2-0 Å2
2---0.003 Å20 Å2
3---0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 424 278 100 802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.018787
X-RAY DIFFRACTIONr_bond_other_d0.0290.023354
X-RAY DIFFRACTIONr_angle_refined_deg2.9842.2881198
X-RAY DIFFRACTIONr_angle_other_deg3.4742.486832
X-RAY DIFFRACTIONr_chiral_restr0.1910.2154
X-RAY DIFFRACTIONr_chiral_restr_other1.620.222
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023136
X-RAY DIFFRACTIONr_nbd_refined0.2190.289
X-RAY DIFFRACTIONr_symmetry_nbd_other0.240.2447
X-RAY DIFFRACTIONr_nbtor_refined0.2530.2301
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.2630.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.263
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.214
X-RAY DIFFRACTIONr_nbd_other0.190.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.216
X-RAY DIFFRACTIONr_scbond_it1.9551.547787
X-RAY DIFFRACTIONr_scbond_other1.9551.557788
X-RAY DIFFRACTIONr_scangle_it3.2142.3051198
X-RAY DIFFRACTIONr_scangle_other3.2132.3161199
X-RAY DIFFRACTIONr_lrange_it5.05913.7951086
X-RAY DIFFRACTIONr_lrange_other5.06513.5921074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6930.317100.245348X-RAY DIFFRACTION42.5684
1.693-1.7390.251130.241394X-RAY DIFFRACTION48.8595
1.739-1.790.345180.223471X-RAY DIFFRACTION61.5094
1.79-1.8450.293340.231584X-RAY DIFFRACTION79.6392
1.845-1.9050.256290.236705X-RAY DIFFRACTION95.8225
1.905-1.9720.36360.231693X-RAY DIFFRACTION99.4543
1.972-2.0460.231350.204678X-RAY DIFFRACTION100
2.046-2.130.239420.204639X-RAY DIFFRACTION100
2.13-2.2250.338420.207611X-RAY DIFFRACTION99.6947
2.225-2.3330.329370.224589X-RAY DIFFRACTION99.523
2.333-2.4590.259310.226568X-RAY DIFFRACTION100
2.459-2.6080.303210.246556X-RAY DIFFRACTION100
2.608-2.7880.374310.26510X-RAY DIFFRACTION100
2.788-3.0110.382350.225472X-RAY DIFFRACTION99.4118
3.011-3.2980.312280.219436X-RAY DIFFRACTION97.8903
3.298-3.6870.276250.2402X-RAY DIFFRACTION98.1609
3.687-4.2560.169260.168338X-RAY DIFFRACTION97.0667
4.256-5.2090.219200.156311X-RAY DIFFRACTION99.3994
5.209-7.3530.232140.196253X-RAY DIFFRACTION99.2565
7.353-28.5620.269150.272138X-RAY DIFFRACTION87.931

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