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- PDB-7ei5: GNRA tetraloop receptor motif composed of RNA and DNA -

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Basic information

Entry
Database: PDB / ID: 7ei5
TitleGNRA tetraloop receptor motif composed of RNA and DNA
ComponentsDNA/RNA (35-MER)
KeywordsDNA-RNA HYBRID / GNRA tetraloop / tetraloop receptor
Function / homology: / STRONTIUM ION / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKondo, J. / Hayasaka, A.
CitationJournal: To Be Published
Title: RNA GNRA tetraloop and tetraloop receptor motifs
Authors: Kondo, J. / Hayasaka, A.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 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

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,65019
Polymers11,1301
Non-polymers1,52018
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-29 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.220, 83.220, 67.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: DNA/RNA hybrid DNA/RNA (35-MER)


Mass: 11129.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, hexammine cobalt, strontium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30.44 Å / Num. obs: 7623 / % possible obs: 98.8 % / Redundancy: 2.669 % / Biso Wilson estimate: 37.566 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.079 / Χ2: 1.057 / Net I/σ(I): 13.75 / Num. measured all: 20349 / Scaling rejects: 2
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
2.9-2.972.4310.2863.313815985680.8720.36695
2.97-3.062.5770.2064.5113455265220.9530.26199.2
3.06-3.142.7890.137.3715705665630.9780.16199.5
3.14-3.242.7510.1028.5913594944940.9890.127100
3.24-3.352.7650.0919.5814685385310.990.11398.7
3.35-3.462.7480.1049.2312864704680.9850.12999.6
3.46-3.62.7440.07511.1413174824800.9940.09399.6
3.6-3.742.7440.0712.0812214504450.9940.08898.9
3.74-3.912.7240.06913.511934384380.9910.086100
3.91-4.12.6720.05415.6411654364360.9940.068100
4.1-4.322.6840.05317.2710013783730.9940.06798.7
4.32-4.582.5530.04517.999833883850.9950.05699.2
4.58-4.92.5680.04220.088683483380.9950.05297.1
4.9-5.292.3690.03621.757963463360.9950.04697.1
5.29-5.82.5510.03423.617322882870.9970.04399.7
5.8-6.482.610.03123.677102742720.9980.03999.3
6.48-7.482.9120.03525.997252502490.9980.04399.6
7.48-9.172.8870.03627.015862042030.9960.04499.5
9.17-12.962.8310.03828.244531601600.9960.047100
12.96-30.442.5330.03729.3719080750.9980.04993.8

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Processing

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

4fnj


Resolution: 2.9→30.44 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 745 9.78 %
Rwork0.1721 6874 -
obs0.1748 7619 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.69 Å2 / Biso mean: 35.5645 Å2 / Biso min: 11.34 Å2
Refinement stepCycle: final / Resolution: 2.9→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 738 19 1 758
Biso mean--101.51 11.34 -
Num. residues----35
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 (%)
2.9-3.120.31111450.26261374151998
3.12-3.440.23551460.1821391153799
3.44-3.930.18071580.16651348150699
3.93-4.950.17911520.141381153399
4.96-30.440.17261440.16391380152499

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