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

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Basic information

Entry
Database: PDB / ID: 7eeo
TitleBulged-G motif composed of RNA, DNA and 2'-O-methyl RNA
ComponentsDNA/RNA (27-MER)
KeywordsDNA-RNA HYBRID / Bulged-G motif / RNA
Function / homologyCOBALT HEXAMMINE(III) / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 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

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Assembly

Deposited unit
A: DNA/RNA (27-MER)
B: DNA/RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1795
Polymers17,6952
Non-polymers4833
Water1448
1
A: DNA/RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1703
Polymers8,8481
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint15 kcal/mol
Surface area3840 Å2
MethodPISA
2
B: DNA/RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0092
Polymers8,8481
Non-polymers1611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint17 kcal/mol
Surface area3600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.776, 116.432, 27.904
Angle α, β, γ (deg.)90.000, 107.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 8847.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium chloride, MPD, hexammine cobalt, lithium 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: 1.60496 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60496 Å / Relative weight: 1
ReflectionResolution: 2.7→29.108 Å / Num. obs: 7521 / % possible obs: 90.3 % / Redundancy: 1.565 % / Biso Wilson estimate: 59.23 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.077 / Χ2: 2.452 / Net I/σ(I): 8.33
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
2.7-2.771.5640.2672.368686515550.8960.37385.3
2.77-2.851.6420.22.828625695250.9450.27992.3
2.85-2.931.5670.1673.397685314900.940.23392.3
2.93-3.021.5880.1544.468595815410.9520.21693.1
3.02-3.121.640.1046.318875865410.980.14592.3
3.12-3.231.5910.096.746974744380.9770.12692.4
3.23-3.351.5590.0697.777225064630.9910.09791.5
3.35-3.491.5730.068.487555304800.9940.08490.6
3.49-3.641.5450.0519.445874283800.9930.07388.8
3.64-3.821.6060.05710.196654504140.9890.07892
3.82-4.031.5250.05511.185844253830.9890.07790.1
4.03-4.271.4930.06711.475244023510.980.09487.3
4.27-4.571.4740.05711.964823773270.9850.0886.7
4.57-4.931.3560.06511.754303653170.9770.09286.8
4.93-5.41.590.04413.554613072900.9920.06194.5
5.4-6.041.5750.04813.964222892680.990.06892.7
6.04-6.971.6280.03914.353892662390.9920.05589.8
6.97-8.541.5380.03614.423002211950.9930.05188.2
8.54-12.081.6060.03314.962281551420.9950.04691.6
12.08-29.1081.520.03214.5611496750.9930.04578.1

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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: 2.701→29.108 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 35.27 / Stereochemistry target values: ML
Details: The Sf file contains friedel pairs under F_plus and F_minus columns.
RfactorNum. reflection% reflection
Rfree0.2648 756 10.05 %
Rwork0.2068 6765 -
obs0.2128 7521 92.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.12 Å2 / Biso mean: 49.5215 Å2 / Biso min: 20.95 Å2
Refinement stepCycle: final / Resolution: 2.701→29.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1023 21 8 1052
Biso mean--62.03 46.46 -
Num. residues----47
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061161
X-RAY DIFFRACTIONf_angle_d1.5311814
X-RAY DIFFRACTIONf_chiral_restr0.063216
X-RAY DIFFRACTIONf_plane_restr0.00747
X-RAY DIFFRACTIONf_dihedral_angle_d18.583445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.701-2.90910.43291470.3563132592
2.9091-3.20150.30461620.2451140394
3.2015-3.6640.25041510.1733137294
3.664-4.61330.20971440.1777132989
4.6133-29.1080.26141520.2053133691

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