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- PDB-7een: Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA -

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Basic information

Entry
Database: PDB / ID: 7een
TitleBulged-G motif composed of RNA, DNA and 2'-O-methyl RNA
ComponentsDNA/RNA (27-MER)
KeywordsDNA-RNA HYBRID / Bulged-G 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: 1.7 Å
AuthorsKondo, J. / Sekiguchi, S.
CitationJournal: To Be Published
Title: Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA
Authors: Kondo, J. / Sekiguchi, S.
History
DepositionMar 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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 (27-MER)
B: DNA/RNA (27-MER)
C: DNA/RNA (27-MER)
D: DNA/RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,73337
Polymers35,4104
Non-polymers1,32333
Water9,566531
1
A: DNA/RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,37414
Polymers8,8531
Non-polymers52113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-17 kcal/mol
Surface area4280 Å2
MethodPISA
2
B: DNA/RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0135
Polymers8,8531
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-19 kcal/mol
Surface area4450 Å2
MethodPISA
3
C: DNA/RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,29312
Polymers8,8531
Non-polymers44111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-3 kcal/mol
Surface area4420 Å2
MethodPISA
4
D: DNA/RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0536
Polymers8,8531
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint2 kcal/mol
Surface area4420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.867, 68.867, 116.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-356-

HOH

21C-267-

HOH

31C-276-

HOH

41C-285-

HOH

51D-257-

HOH

61D-268-

HOH

71D-276-

HOH

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Components

#1: DNA/RNA hybrid
DNA/RNA (27-MER)


Mass: 8852.521 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 1.94 Å3/Da / Density % sol: 36.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, calcium 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: 1.7→30.28 Å / Num. obs: 30956 / % possible obs: 98.2 % / Redundancy: 6.522 % / Biso Wilson estimate: 25.243 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.093 / Χ2: 0.98 / Net I/σ(I): 11.97 / Num. measured all: 201904 / Scaling rejects: 12
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
1.7-1.746.8050.3654.715285228422460.940.39498.3
1.74-1.796.890.315.4315123222021950.9570.33498.9
1.79-1.846.8210.2776.1414699216921550.9610.29799.4
1.84-1.96.7210.246.8414195212021120.9720.25899.6
1.9-1.966.6390.2357.2513583205220460.9680.25399.7
1.96-2.036.5020.1848.6412821199019720.980.19899.1
2.03-2.116.5040.1549.9812370191619020.9860.16799.3
2.11-2.196.2350.13810.4611398184818280.9890.1598.9
2.19-2.295.6730.13310.5310008177617640.9870.14599.3
2.29-2.45.6970.11611.759565169716790.990.12798.9
2.4-2.535.9160.09813.449584163416200.9940.10799.1
2.53-2.696.8020.08915.8310250153415070.9950.09598.2
2.69-2.876.9010.07917.689875147314310.9960.08597.1
2.87-3.16.8380.07119.838951134813090.9960.07697.1
3.1-3.46.8130.06221.38298126512180.9970.06796.3
3.4-3.86.7310.06322.187404114711000.9920.06995.9
3.8-4.396.590.06122.87656410359960.9930.06696.2
4.39-5.376.6040.05722.8755218838360.9980.06194.7
5.37-7.66.3930.05322.5242647096670.9980.05694.1
7.6-30.285.7530.05521.1921464283730.9980.0687.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q9A

1q9a


Resolution: 1.7→30.28 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1998 6.46 %
Rwork0.1885 28943 -
obs0.1915 30941 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.5 Å2 / Biso mean: 21.0919 Å2 / Biso min: 8.84 Å2
Refinement stepCycle: final / Resolution: 1.7→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2279 33 531 2843
Biso mean--30.29 27.07 -
Num. residues----105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.740.28011400.21972028216898
1.74-1.790.24251400.21232026216699
1.79-1.840.26181420.20772060220299
1.84-1.90.27161430.210620682211100
1.9-1.970.27691430.218820732216100
1.97-2.050.26561420.21192052219499
2.05-2.140.25421430.2022069221299
2.14-2.250.24491410.21322044218599
2.25-2.390.27921440.22322080222499
2.39-2.580.2441440.21992091223599
2.58-2.840.28531430.21672067221098
2.84-3.250.22911410.17452059220096
3.25-4.090.19551450.14392082222796
4.09-30.280.19451470.16382144229194

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