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- PDB-7bpg: Structure of serinol nucleic acid - RNA complex -

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Basic information

Entry
Database: PDB / ID: 7bpg
TitleStructure of serinol nucleic acid - RNA complex
Components
  • RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
  • SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)
KeywordsRNA/NUCLEIC ACID / Xeno nucleic acid / artificial nucleic acid / acyclic nucleic acid / serinol nucleic acid / RNA / RNA-NUCLEIC ACID complex
Function / homologyDNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKamiya, Y. / Satoh, T. / Kodama, A. / Suzuki, T. / Uchiyama, S. / Kato, K. / Asanuma, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Commun Chem / Year: 2020
Title: Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA
Authors: Kamiya, Y. / Satoh, T. / Kodama, A. / Suzuki, T. / Murayama, K. / Kashida, H. / Uchiyama, S. / Kato, K. / Asanuma, H.
History
DepositionMar 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
C: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
E: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
G: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
B: SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)
D: SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)
F: SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)
H: SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3379
Polymers20,2978
Non-polymers401
Water1,18966
1
A: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
B: SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1143
Polymers5,0742
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
D: SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)


Theoretical massNumber of molelcules
Total (without water)5,0742
Polymers5,0742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
F: SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)


Theoretical massNumber of molelcules
Total (without water)5,0742
Polymers5,0742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
H: SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)


Theoretical massNumber of molelcules
Total (without water)5,0742
Polymers5,0742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.363, 46.918, 47.540
Angle α, β, γ (deg.)90.00, 114.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain
RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')


Mass: 2597.433 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain
SNA (S-(F7R)(F7X)(F7O)(F7R)(F7X)(F7O)(F7R)(F7U)-R)


Mass: 2476.757 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 400, 0.1M HEPES (pH6.5), 75mM Calcium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.919744 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919744 Å / Relative weight: 1
ReflectionResolution: 1.7→46.92 Å / Num. obs: 17920 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Net I/σ(I): 14.3
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2 / Num. unique obs: 917 / CC1/2: 0.734 / Rpim(I) all: 0.6 / Rrim(I) all: 1.144 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 20.339 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 894 5 %RANDOM
Rwork0.232 ---
obs0.234 16997 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.738 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å2-0 Å23.56 Å2
2---6.54 Å2-0 Å2
3---3.71 Å2
Refinement stepCycle: 1 / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 648 681 66 1395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0161446
X-RAY DIFFRACTIONr_bond_other_d0.0070.021682
X-RAY DIFFRACTIONr_angle_refined_deg1.5682.0362054
X-RAY DIFFRACTIONr_angle_other_deg19.9193.0211544
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_restr0.0710.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02785
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02242
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_it4.9926.0441446
X-RAY DIFFRACTIONr_scbond_other4.9076.0591331
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4129.1111885
X-RAY DIFFRACTIONr_long_range_B_refined8.36358.7682262
X-RAY DIFFRACTIONr_long_range_B_other8.29858.4932233
X-RAY DIFFRACTIONr_rigid_bond_restr3.92932128
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 62 -
Rwork0.351 1216 -
obs--99.77 %

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