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- PDB-6u89: RNA duplex, bound with TNA monomer -

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Basic information

Entry
Database: PDB / ID: 6u89
TitleRNA duplex, bound with TNA monomer
ComponentsRNA (5'-R(*(LCC)P*(TLN)P*(LCG)P*UP*AP*CP*A)-3')
KeywordsRNA
Function / homologyChem-TG / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsSzostak, J.W. / Zhang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization.
Authors: Zhang, W. / Kim, S.C. / Tam, C.P. / Lelyveld, V.S. / Bala, S. / Chaput, J.C. / Szostak, J.W.
History
DepositionSep 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 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*(TLN)P*(LCG)P*UP*AP*CP*A)-3')
B: RNA (5'-R(*(LCC)P*(TLN)P*(LCG)P*UP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1554
Polymers4,4912
Non-polymers6642
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint15 kcal/mol
Surface area2920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.892, 51.892, 37.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: RNA chain RNA (5'-R(*(LCC)P*(TLN)P*(LCG)P*UP*AP*CP*A)-3')


Mass: 2245.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TG / 2-azanyl-9-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]-1~{H}-purin-6-one


Type: RNA linking / Mass: 332.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.28 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25 % v/v Polyethylene glycol 400, 100 mM tri-Sodium citrate; pH 5.6, 130 mM Sodium chloride, 60 mM Magnesium chloride

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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: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 2444 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.933 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.086 / Rrim(I) all: 0.185 / Χ2: 1 / Net I/σ(I): 10.67
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 228 / CC1/2: 0.753 / Rpim(I) all: 0.307 / Rrim(I) all: 0.621 / Χ2: 0.549 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HBW

5hbw


Resolution: 2.36→44.96 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.274 113 4.6 %random
Rwork0.188 ---
obs0.191 2331 99.96 %-
Displacement parametersBiso mean: 36.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.36→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 298 44 4 346
LS refinement shellResolution: 2.36→2.43 Å
RfactorNum. reflection% reflection
Rfree0.461 7 -
Rwork0.298 155 -
obs--99.39 %

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