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- PDB-7ecl: RNA duplex containing C-Ag-A and U-Ag-A base pair -

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Basic information

Entry
Database: PDB / ID: 7ecl
TitleRNA duplex containing C-Ag-A and U-Ag-A base pair
ComponentsDNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*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: 3.01 Å
AuthorsKondo, J. / Uchida, Y.
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-A and U-Ag-A base pair
Authors: Kondo, J. / Uchida, Y.
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
A: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
B: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
C: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
D: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
E: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
F: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
G: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
H: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
I: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
J: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
K: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
L: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,97235
Polymers46,49112
Non-polymers2,48123
Water00
1
A: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
B: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1806
Polymers7,7482
Non-polymers4314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-21 kcal/mol
Surface area4040 Å2
MethodPISA
2
C: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
D: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2887
Polymers7,7482
Non-polymers5395
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-30 kcal/mol
Surface area4010 Å2
MethodPISA
3
E: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
F: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0725
Polymers7,7482
Non-polymers3243
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-19 kcal/mol
Surface area4060 Å2
MethodPISA
4
G: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
H: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1806
Polymers7,7482
Non-polymers4314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-24 kcal/mol
Surface area4070 Å2
MethodPISA
5
I: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
J: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0725
Polymers7,7482
Non-polymers3243
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-17 kcal/mol
Surface area4060 Å2
MethodPISA
6
K: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
L: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1806
Polymers7,7482
Non-polymers4314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-24 kcal/mol
Surface area3960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.252, 43.252, 378.967
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: RNA chain
DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')


Mass: 3874.232 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical...
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Ag
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: 2.2 Å3/Da / Density % sol: 44.12 %
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-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.01→42.11 Å / Num. obs: 9049 / % possible obs: 99.5 % / Redundancy: 4.617 % / Biso Wilson estimate: 63.491 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.092 / Χ2: 0.907 / Net I/σ(I): 10.6 / Num. measured all: 41779
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
3.01-3.084.910.333.232856816690.9930.3798.2
3.08-3.174.8380.2214.1728405905870.9920.2599.5
3.17-3.265.0660.2165.2231566286230.990.24199.2
3.26-3.364.8950.1935.529476066020.9890.21699.3
3.36-3.474.7140.1446.4626825695690.9960.162100
3.47-3.594.9760.1646.429315895890.9980.184100
3.59-3.734.4930.1177.8223505245230.9960.13399.8
3.73-3.884.5280.1198.7224185375340.9960.13599.4
3.88-4.054.0580.0979.7719684884850.9960.11199.4
4.05-4.254.5680.111.7523075065050.9940.11399.8
4.25-4.484.8620.08414.3721784494480.9940.09599.8
4.48-4.754.4180.07714.0621034784760.9970.08899.6
4.75-5.084.1490.07614.5416183923900.9950.08799.5
5.08-5.494.6360.06217.4419474204200.9970.07100
5.49-6.014.7920.06818.0717303613610.9960.076100
6.01-6.724.6480.06317.0315713383380.9980.069100
6.72-7.764.450.05820.4713663073070.9970.065100
7.76-9.514.2210.0521.3711482732720.9970.05899.6
9.51-13.453.8330.04321.788242162150.9990.04999.5
13.45-42.113.0150.02819.8441014113610.03496.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→42.11 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2925 891 9.98 %
Rwork0.2184 8041 -
obs0.2255 8932 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.95 Å2 / Biso mean: 55.7474 Å2 / Biso min: 29.89 Å2
Refinement stepCycle: final / Resolution: 3.01→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3024 23 0 3047
Biso mean--71.5 --
Num. residues----144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.01-3.190.36481420.28451251139396
3.19-3.440.34521420.27091294143697
3.44-3.790.35521500.27811293144398
3.79-4.330.3251550.23941343149899
4.33-5.450.30781510.22661372152399
5.46-42.110.2121510.15451488163999

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