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- PDB-5uef: RNA primer-template complex with guanosine dinucleotide p(5')G(3'... -

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Basic information

Entry
Database: PDB / ID: 5uef
TitleRNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand
Components
  • RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
  • RNA (5'-R(P*GP*G)-3')
KeywordsRNA / dinucleotide
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, W. / Tam, C.P. / Szostak, J.W.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex.
Authors: Zhang, W. / Tam, C.P. / Walton, T. / Fahrenbach, A.C. / Birrane, G. / Szostak, J.W.
History
DepositionJan 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
B: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
C: RNA (5'-R(P*GP*G)-3')
D: RNA (5'-R(P*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)10,2924
Polymers10,2924
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint2 kcal/mol
Surface area5830 Å2
Unit cell
Length a, b, c (Å)43.628, 43.628, 84.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

21A-102-

HOH

31B-101-

HOH

41B-103-

HOH

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Components

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


Mass: 4500.794 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(P*GP*G)-3')


Mass: 645.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M Magnesium chloride, 0.1 M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 5804 / % possible obs: 99.8 % / Redundancy: 9.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.074 / Net I/σ(I): 30.86
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.78 / CC1/2: 0.885 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DHC

5dhc


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.427 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.235 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30318 297 5.2 %RANDOM
Rwork0.23967 ---
obs0.24289 5391 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.671 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 690 0 8 698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.014766
X-RAY DIFFRACTIONr_bond_other_d0.0270.022336
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.5891188
X-RAY DIFFRACTIONr_angle_other_deg3.6933.144810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02388
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021156
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7054.933765
X-RAY DIFFRACTIONr_scbond_other3.7084.932764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2177.4061189
X-RAY DIFFRACTIONr_long_range_B_refined8.97749.9181121
X-RAY DIFFRACTIONr_long_range_B_other8.97349.9261122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.096→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 9 -
Rwork0.363 384 -
obs--97.04 %

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