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- PDB-7efi: RNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA -

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Basic information

Entry
Database: PDB / ID: 7efi
TitleRNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA
ComponentsDNA/RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*(OMG)P*(OMG)P*(OMG))-D(P*GP*A)-R(P*GP*(OMC)P*(OMC))-3')
KeywordsDNA-RNA HYBRID / Kink-turn motif / RNA
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKondo, J. / Nagashima, M.
CitationJournal: To Be Published
Title: RNA kink-turn motif composed of RNA, DNA and 2'-O-methyl RNA
Authors: Kondo, J. / Nagashima, M.
History
DepositionMar 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 2.0May 11, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / refine_ls_shell / struct_asym / struct_conn
Item: _atom_site.auth_seq_id / _atom_site.label_asym_id ..._atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _ndb_struct_conf_na.feature / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*(OMG)P*(OMG)P*(OMG))-D(P*GP*A)-R(P*GP*(OMC)P*(OMC))-3')


Theoretical massNumber of molelcules
Total (without water)6,2721
Polymers6,2721
Non-polymers00
Water00
1
A: DNA/RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*(OMG)P*(OMG)P*(OMG))-D(P*GP*A)-R(P*GP*(OMC)P*(OMC))-3')

A: DNA/RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*(OMG)P*(OMG)P*(OMG))-D(P*GP*A)-R(P*GP*(OMC)P*(OMC))-3')


Theoretical massNumber of molelcules
Total (without water)12,5442
Polymers12,5442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_769-x+2,-x+y+1,-z+41
Unit cell
Length a, b, c (Å)70.565, 70.565, 48.165
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*(OMG)P*(OMG)P*(OMG))-D(P*GP*A)-R(P*GP*(OMC)P*(OMC))-3')


Mass: 6271.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→37.83 Å / Num. obs: 1761 / % possible obs: 98.5 % / Redundancy: 4.528 % / Biso Wilson estimate: 60.417 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.065 / Χ2: 0.97 / Net I/σ(I): 16.91 / Num. measured all: 7974
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.984.4510.3663.986321431420.9560.41599.3
2.98-3.074.2480.2185.755651351330.9870.24898.5
3.07-3.174.4920.1577.125841341300.9920.17897
3.17-3.284.8620.13110.665981261230.990.14697.6
3.28-3.414.960.09811.996251261260.9970.109100
3.41-3.554.9160.07314.855851201190.9980.08199.2
3.55-3.714.8310.07615.175701181180.9980.085100
3.71-3.894.8770.05619.155171061060.9980.063100
3.89-4.14.7040.048205081091080.9980.05599.1
4.1-4.354.6950.05321.9344696950.9980.06199
4.35-4.654.6560.04925.3944796960.9970.055100
4.65-5.024.4890.04823.0342295940.9970.05598.9
5.02-5.54.0490.03925.1433282820.9990.044100
5.5-6.153.6880.04524.6528479770.9970.05397.5
6.15-7.14.2470.04328.4631073730.9970.049100
7.1-8.694.3440.03629.7626562610.9990.04198.4
8.69-12.293.90.04432.6919553500.9970.05194.3
12.29-37.833.1790.0328.0489342810.03582.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CS1

4cs1


Resolution: 2.9→37.83 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 177 10.1 %
Rwork0.1924 1576 -
obs0.1968 1753 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.35 Å2 / Biso mean: 56.7454 Å2 / Biso min: 38.77 Å2
Refinement stepCycle: final / Resolution: 2.9→37.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 375 42 0 417
Biso mean--53.73 --
Num. residues----17

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