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- PDB-7ecm: RNA duplex containing C-A base pair -

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Basic information

Entry
Database: PDB / ID: 7ecm
TitleRNA duplex containing C-A base pair
ComponentsRNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
KeywordsRNA / mismatch / Barium
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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-A base pair
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*AP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
C: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,60113
Polymers15,3654
Non-polymers1,2369
Water4,234235
1
A: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2326
Polymers7,6832
Non-polymers5494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-48 kcal/mol
Surface area4160 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
D: RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3697
Polymers7,6832
Non-polymers6875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-51 kcal/mol
Surface area4300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.475, 27.909, 46.665
Angle α, β, γ (deg.)100.080, 93.540, 110.470
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 3841.368 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MOPS, MPD, spermine, barium 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: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.51→45.54 Å / Num. obs: 18436 / % possible obs: 95.4 % / Redundancy: 3.635 % / Biso Wilson estimate: 21.271 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.067 / Χ2: 0.997 / Net I/σ(I): 13.37
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
1.51-1.553.7110.2765.515003148013480.930.32391.1
1.55-1.593.7170.2266.364665134312550.9540.26593.4
1.59-1.633.7380.1577.814889139313080.9850.18493.9
1.63-1.683.7220.1378.794518128912140.9820.1694.2
1.68-1.743.7390.1149.964625130812370.990.13394.6
1.74-1.83.720.10710.754267121011470.9870.12594.8
1.8-1.873.6360.09611.294149120211410.9880.11394.9
1.87-1.953.5510.09111.883881113910930.9880.10896
1.95-2.033.40.08113.183587110510550.9880.09795.5
2.03-2.133.1670.06913.64312310269860.9910.08496.1
2.13-2.253.5110.06915.52336710019590.9930.08295.8
2.25-2.383.3280.06416.3230729629230.9910.07795.9
2.38-2.553.8220.06118.3732608708530.9930.0798
2.55-2.753.8310.05820.0431038278100.9940.06897.9
2.75-3.013.7540.04721.2327377527290.9980.05496.9
3.01-3.373.7370.03822.4825456916810.9990.04498.6
3.37-3.893.760.04423.3622866206080.9970.05298.1
3.89-4.773.7570.04623.7818264934860.9970.05398.6
4.77-6.743.5680.04923.2413954003910.9950.05797.8
6.74-45.543.40.0522.977142172100.9950.0696.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→45.54 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 2.08 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 1835 9.95 %
Rwork0.1573 16601 -
obs0.1611 18436 95.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.69 Å2 / Biso mean: 16.0267 Å2 / Biso min: 6.83 Å2
Refinement stepCycle: final / Resolution: 1.51→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1016 9 235 1260
Biso mean--44.32 23.79 -
Num. residues----48
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 (%)
1.51-1.550.27491410.22611255139690
1.55-1.590.23151270.19631209133694
1.59-1.640.20131310.16581294142593
1.64-1.70.18771490.16121235138496
1.7-1.770.19041400.14411264140493
1.77-1.850.19371390.15741300143996
1.85-1.950.21451450.16271274141995
1.95-2.070.20111390.16531267140695
2.07-2.230.18761460.16821284143096
2.23-2.460.19551370.1681282141997
2.46-2.810.23091490.1681337148698
2.81-3.540.19851450.15681290143598
3.54-45.540.1611470.12831310145798

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