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- PDB-6owl: RNA oligonucleotides with 3'-arabino guanosine co-crystallized wi... -

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Basic information

Entry
Database: PDB / ID: 6owl
TitleRNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP
Components
  • RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*R)-3')
  • RNA (5'-R(P*G)-3')
KeywordsRNA / arabino
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSzostak, J.W. / Kim, S. / Zhang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides.
Authors: Kim, S.C. / Zhou, L. / Zhang, W. / O'Flaherty, D.K. / Rondo-Brovetto, V. / Szostak, J.W.
History
DepositionMay 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,8043
Polymers5,8043
Non-polymers00
Water1448
1
A: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*R)-3')
B: RNA (5'-R(P*G)-3')
C: RNA (5'-R(P*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)11,6076
Polymers11,6076
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_647y+1,x-1,-z+21
Unit cell
Length a, b, c (Å)43.483, 43.483, 127.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 4512.804 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: RNA chain RNA (5'-R(P*G)-3')


Mass: 645.454 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: 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 Å3/Da / Density % sol: 38.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.08 M Sodium chloride, 0.012 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 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: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 3409 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.982 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.09 / Χ2: 0.831 / Net I/σ(I): 19.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 332 / CC1/2: 0.94 / Rrim(I) all: 0.627 / Χ2: 0.539 / % possible all: 100

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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: 6C8D

6c8d


Resolution: 2→22 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.49 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31721 158 4.7 %RANDOM
Rwork0.237 ---
obs0.24152 3229 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.933 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 347 0 8 355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.016388
X-RAY DIFFRACTIONr_bond_other_d0.0380.023168
X-RAY DIFFRACTIONr_angle_refined_deg2.281.836606
X-RAY DIFFRACTIONr_angle_other_deg3.7563.198402
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_restr0.1110.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02186
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0266
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_it3.8544.421386
X-RAY DIFFRACTIONr_scbond_other3.8454.424385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8026.623605
X-RAY DIFFRACTIONr_long_range_B_refined10.18139.499511
X-RAY DIFFRACTIONr_long_range_B_other10.18339.396511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 10 -
Rwork0.263 191 -
obs--85.9 %

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