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- PDB-7ecp: RNA duplex containing C-Ag-U -

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Basic information

Entry
Database: PDB / ID: 7ecp
TitleRNA duplex containing C-Ag-U
ComponentsRNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*UP*CP*CP*C)-3')
KeywordsRNA / Metal-mediated base pair / Silver
Function / homologySILVER ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 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 C-Ag-U
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7058
Polymers15,2734
Non-polymers4314
Water905
1
A: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*UP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*UP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8524
Polymers7,6372
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-27 kcal/mol
Surface area4320 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*UP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*UP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8524
Polymers7,6372
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-26 kcal/mol
Surface area4330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.968, 88.968, 33.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 3818.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
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: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.91→31.45 Å / Num. obs: 2968 / % possible obs: 99.3 % / Redundancy: 3.688 % / Biso Wilson estimate: 16.957 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.11 / Χ2: 0.952 / Net I/σ(I): 9.9 / Num. measured all: 10945
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.91-2.993.6460.2044.472230.9890.23698.2
2.99-3.073.670.1425.662120.9920.16499.5
3.07-3.163.4950.1156.262040.9940.134100
3.16-3.263.3370.0987.622050.9950.11599.5
3.26-3.363.3570.0757.61820.9970.08898.9
3.36-3.483.6120.1267.471880.9910.146100
3.48-3.613.4890.0879.481860.9940.101100
3.61-3.763.5650.0879.91610.9950.09999.4
3.76-3.933.7090.0849.421720.9960.096100
3.93-4.124.1350.09710.981630.9930.111100
4.12-4.343.9550.10311.781540.9890.119100
4.34-4.614.0970.10712.641440.9870.12599.3
4.61-4.923.8990.09612.591380.9870.11299.3
4.92-5.323.9040.07214.391250.9940.08498.4
5.32-5.833.9420.07612.911210.9950.08999.2
5.83-6.513.9650.08912.421140.9940.104100
6.51-7.523.80.06714.78900.9920.07998.9
7.52-9.213.6460.0614.59820.9960.071100
9.21-13.033.4330.05220.36670.9960.06295.7
13.03-31.452.8920.03920.44370.9990.04792.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→31.45 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 13.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 293 10.07 %
Rwork0.1536 2618 -
obs0.1608 2911 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.54 Å2 / Biso mean: 17.2673 Å2 / Biso min: 1.16 Å2
Refinement stepCycle: final / Resolution: 2.91→31.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1008 4 5 1017
Biso mean--31.45 9.65 -
Num. residues----48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.91-3.660.25781440.19521264140896
3.67-31.450.2051490.12741354150399

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