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- PDB-7m3v: RNA bulged-G motif -

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Basic information

Entry
Database: PDB / ID: 7m3v
TitleRNA bulged-G motif
ComponentsRNA (27-MER)
KeywordsRNA / Bulged-G motif
Function / homologyIRIDIUM (III) ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKondo, J. / Sekiguchi, S.
CitationJournal: To Be Published
Title: RNA bulged-G motif
Authors: Kondo, J. / Sekiguchi, S.
History
DepositionMar 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9362
Polymers8,7441
Non-polymers1921
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.657, 29.657, 76.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: RNA chain RNA (27-MER)


Mass: 8744.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-IR3 / IRIDIUM (III) ION


Mass: 192.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ir
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.93 Å3/Da / Density % sol: 36.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MOPS, ammonium sulfate, magnesium 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: 1.10567 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10567 Å / Relative weight: 1
ReflectionResolution: 2.19→27.66 Å / Num. obs: 6691 / % possible obs: 99.8 % / Redundancy: 6.761 % / Biso Wilson estimate: 30.31 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.128 / Χ2: 1.71 / Net I/σ(I): 13.64 / Num. measured all: 45236
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
2.19-2.255.9920.3357.2229965125000.9320.36897.7
2.25-2.316.5140.3367.3931204794790.9540.368100
2.31-2.386.6490.3448.5230124534530.9330.375100
2.38-2.456.6330.289.4232374884880.9540.304100
2.45-2.537.0220.24210.8931254454450.9760.262100
2.53-2.627.1270.20811.0229154094090.9860.224100
2.62-2.727.0020.16412.6328504074070.9880.177100
2.72-2.836.8820.13513.0628084084080.9910.146100
2.83-2.966.440.12813.224733843840.9920.139100
2.96-3.16.3970.10115.2521753403400.9970.111100
3.1-3.277.1170.09617.4127333843840.9950.103100
3.27-3.477.1590.118.3322553153150.9940.108100
3.47-3.717.1610.09718.5221773043040.9940.105100
3.71-4.017.20.08619.8319442702700.9950.093100
4.01-4.397.0070.08819.5218782682680.9920.095100
4.39-4.916.8890.0919.8816812442440.9910.097100
4.91-5.676.1880.08919.6412502022020.9910.097100
5.67-6.946.5460.07920.312111851850.9940.086100
6.94-9.827.0430.08321.489721381380.9860.09100
9.82-27.666.2350.07920.4542469680.9970.08798.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q9A

1q9a


Resolution: 2.19→27.66 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 655 9.79 %
Rwork0.1774 6036 -
obs0.1814 6691 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.45 Å2 / Biso mean: 17.4367 Å2 / Biso min: 4.18 Å2
Refinement stepCycle: final / Resolution: 2.19→27.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 579 1 49 629
Biso mean--56.92 22.72 -
Num. residues----27
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.360.37771280.34611203133198
2.36-2.60.3091340.24512091343100
2.6-2.970.28021380.198912071345100
2.98-3.740.15431270.13112051332100
3.75-27.660.13971280.119612121340100

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