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- PDB-7eco: RNA duplex containing U-Ag-U base pairs -

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Basic information

Entry
Database: PDB / ID: 7eco
TitleRNA duplex containing U-Ag-U base pairs
ComponentsRNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
KeywordsRNA / metal-mediated base pairs / silver
Function / homologySILVER ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKondo, J. / Tsudura, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24245037 Japan
CitationJournal: To Be Published
Title: RNA duplex containing U-Ag-U base pairs
Authors: Kondo, J. / Tsudura, A.
History
DepositionMar 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
F: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
A: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
C: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,56312
Polymers22,9166
Non-polymers6476
Water3,765209
1
E: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
F: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8544
Polymers7,6392
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-27 kcal/mol
Surface area4320 Å2
MethodPISA
2
A: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8544
Polymers7,6392
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-27 kcal/mol
Surface area4330 Å2
MethodPISA
3
C: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*UP*CP*CP*GP*GP*UP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8544
Polymers7,6392
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-27 kcal/mol
Surface area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.771, 26.875, 78.944
Angle α, β, γ (deg.)90.000, 101.690, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3819.312 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MOPS, MPD, spermine, lithium nitrate

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.81→36.91 Å / Num. obs: 18483 / % possible obs: 99.7 % / Redundancy: 6.437 % / Biso Wilson estimate: 33.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.064 / Χ2: 0.952 / Net I/σ(I): 17.77 / Num. measured all: 118980
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.81-1.866.0540.3885.1613500.9710.42599.2
1.86-1.916.4610.3166.2413340.9790.344100
1.91-1.966.2680.2617.2212520.990.28599.8
1.96-2.026.8140.2168.9812730.990.23499.9
2.02-2.096.9320.17910.7212050.9930.19499.8
2.09-2.166.8530.16411.8911670.9920.177100
2.16-2.246.7940.1413.8311350.9920.152100
2.24-2.336.7230.10616.3410740.9960.11599.6
2.33-2.446.6250.08918.9710480.9950.09799.6
2.44-2.566.1630.08619.19820.9960.09499.8
2.56-2.76.1850.07521.699660.9950.08299.8
2.7-2.866.180.06524.398990.9970.07299.6
2.86-3.066.6280.04828.78600.9990.052100
3.06-3.36.5080.04930.768070.9980.05399.6
3.3-3.626.2280.04731.557190.9970.051100
3.62-4.046.1680.04332.626780.9990.047100
4.04-4.675.830.04132.815870.9970.04597.7
4.67-5.725.7140.04331.815040.9980.04798.8
5.72-8.096.3560.03933.594070.9990.042100
8.09-36.915.750.0432.812360.9990.04497.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→36.91 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 1843 10 %
Rwork0.185 16590 -
obs0.1882 18433 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.95 Å2 / Biso mean: 27.4564 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 1.81→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1512 6 209 1727
Biso mean--26.58 31.38 -
Num. residues----72
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.860.3291390.261243138299
1.86-1.910.26521420.249512881430100
1.91-1.970.28641390.221912391378100
1.97-2.040.27571410.218112681409100
2.04-2.120.25021400.223312601400100
2.13-2.220.2861420.224112791421100
2.22-2.340.28361400.209612611401100
2.34-2.490.24071430.205812881431100
2.49-2.680.24971420.221512671409100
2.68-2.950.21921410.216412731414100
2.95-3.370.20231420.17951281142399
3.37-4.250.18761430.14881296143999
4.25-36.910.15331490.13311347149698

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