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- PDB-7efh: RNA kink-turn motif -

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Basic information

Entry
Database: PDB / ID: 7efh
TitleRNA kink-turn motif
ComponentsRNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
KeywordsRNA / Kink-turn motif
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKondo, J. / Nagashima, M.
CitationJournal: To Be Published
Title: RNA kink-turn motif
Authors: Kondo, J. / Nagashima, M.
History
DepositionMar 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2341
Polymers6,2341
Non-polymers00
Water1448
1
A: RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')

A: RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)12,4682
Polymers12,4682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/21
Buried area2620 Å2
ΔGint1 kcal/mol
Surface area6140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.434, 51.434, 44.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-108-

HOH

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Components

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


Mass: 6233.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, 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: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→25.72 Å / Num. obs: 1843 / % possible obs: 99.5 % / Redundancy: 5.929 % / Biso Wilson estimate: 35.708 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Χ2: 0.988 / Net I/σ(I): 20.23
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
2.7-2.785.6760.3585.087891421390.9660.39497.9
2.78-2.8660.296.858761461460.970.317100
2.86-2.966.3280.18910.098671371370.9860.206100
2.96-3.066.3490.16212.328001261260.9870.177100
3.06-3.186.4250.11615.498611341340.9960.127100
3.18-3.36.2130.09616.847891271270.9960.105100
3.3-3.456.1360.08218.667241181180.9970.09100
3.45-3.625.8780.07822.146761151150.9960.086100
3.62-3.825.890.06521.876421091090.9980.072100
3.82-4.056.1420.05325.916511061060.9990.058100
4.05-4.336.310.04729.676311001000.9980.052100
4.33-4.676.0110.0529.0256595940.9980.05598.9
4.67-5.125.4270.04430.9148389890.9990.049100
5.12-5.725.1980.04132.2142181810.9980.045100
5.72-6.615.7920.04632.1241772720.9980.051100
6.61-8.095.4920.0432.9834663630.9990.045100
8.09-11.454.6110.03435.1124954540.9960.039100
11.45-25.724.1880.02937.3413437320.9990.03486.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CS1

4cs1


Resolution: 2.7→25.72 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 185 10.04 %
Rwork0.229 1658 -
obs0.2307 1843 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.33 Å2 / Biso mean: 31.6144 Å2 / Biso min: 8.81 Å2
Refinement stepCycle: final / Resolution: 2.7→25.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 414 0 8 422
Biso mean---24.62 -
Num. residues----19
LS refinement shellResolution: 2.7→25.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2461 185 -
Rwork0.229 1658 -
all-1843 -
obs--100 %

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