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- PDB-7u8a: Product of 14mer primer with activated G monomer diastereomer 2 -

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Basic information

Entry
Database: PDB / ID: 7u8a
TitleProduct of 14mer primer with activated G monomer diastereomer 2
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: 2.1 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)10,5989
Polymers9,5882
Non-polymers1,0107
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.873, 42.873, 82.763
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-102-

MG

21B-102-

MG

31A-211-

HOH

41B-207-

HOH

51B-212-

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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM PIPES pH 7.0, 65 mM Magnesium chloride, 1 mM Cobalt (III) Hexamine chloride, 26% v/v (+/-)-2-Methyl-2,4-pentanediol

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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: 2.1→50 Å / Num. obs: 5553 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.026 / Rrim(I) all: 0.083 / Net I/σ(I): 25.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 273 / CC1/2: 0.935 / CC star: 0.983 / Rpim(I) all: 0.175 / Rrim(I) all: 0.556 / % possible all: 100

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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: 2.1→41.416 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.933 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.229
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2818 291 5.248 %
Rwork0.1991 5254 -
all0.203 --
obs-5545 99.659 %
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: 23.632 Å2
Baniso -1Baniso -2Baniso -3
1--0.004 Å2-0.002 Å2-0 Å2
2---0.004 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 424 283 54 761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.018788
X-RAY DIFFRACTIONr_bond_other_d0.0250.023354
X-RAY DIFFRACTIONr_angle_refined_deg2.7062.2881200
X-RAY DIFFRACTIONr_angle_other_deg3.492.486832
X-RAY DIFFRACTIONr_chiral_restr0.1940.2154
X-RAY DIFFRACTIONr_chiral_restr_other1.6040.222
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023136
X-RAY DIFFRACTIONr_nbd_refined0.1420.2106
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2460.2469
X-RAY DIFFRACTIONr_nbtor_refined0.2420.2323
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.260.2190
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.244
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.222
X-RAY DIFFRACTIONr_nbd_other0.210.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.214
X-RAY DIFFRACTIONr_scbond_it2.142.46787
X-RAY DIFFRACTIONr_scbond_other2.1392.469788
X-RAY DIFFRACTIONr_scangle_it3.0413.6761200
X-RAY DIFFRACTIONr_scangle_other3.0393.6841201
X-RAY DIFFRACTIONr_lrange_it5.823.4851123
X-RAY DIFFRACTIONr_lrange_other5.77323.3661108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.303210.213371X-RAY DIFFRACTION97.5124
2.15-2.2090.315230.206356X-RAY DIFFRACTION100
2.209-2.2730.304150.199378X-RAY DIFFRACTION100
2.273-2.3430.257210.206332X-RAY DIFFRACTION99.7175
2.343-2.420.261170.193348X-RAY DIFFRACTION100
2.42-2.5050.313180.218332X-RAY DIFFRACTION100
2.505-2.5990.3680.23319X-RAY DIFFRACTION100
2.599-2.7050.473100.252323X-RAY DIFFRACTION100
2.705-2.8250.415160.3292X-RAY DIFFRACTION100
2.825-2.9630.332190.256272X-RAY DIFFRACTION100
2.963-3.1230.332270.19266X-RAY DIFFRACTION99.6599
3.123-3.3120.238240.197247X-RAY DIFFRACTION99.6324
3.312-3.5410.154130.19242X-RAY DIFFRACTION99.6094
3.541-3.8240.268130.149226X-RAY DIFFRACTION99.5833
3.824-4.1880.29990.151217X-RAY DIFFRACTION100
4.188-4.6810.298150.141197X-RAY DIFFRACTION100
4.681-5.4020.148100.191174X-RAY DIFFRACTION100
5.402-6.6090.18640.193154X-RAY DIFFRACTION100
6.609-9.3170.67830.239132X-RAY DIFFRACTION100
9.317-41.4160.32850.18776X-RAY DIFFRACTION95.2941

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