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- PDB-7edm: Crystal structure of the eukaryotic ribosomal decoding site in co... -

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Basic information

Entry
Database: PDB / ID: 7edm
TitleCrystal structure of the eukaryotic ribosomal decoding site in complex with G418 and Hg(II)
ComponentsRNA (5'-R(P*UP*GP*CP*GP*UP*CP*GP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / Metal-mediated base pair / Mercury / Decoding site / Ribosomal RNA
Function / homologyGENETICIN / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsKondo, J. / Suzuki, C.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24245037 Japan
CitationJournal: To Be Published
Title: Crystal structure of the eukaryotic ribosomal decoding site in complex with G418 and Hg(II)
Authors: Kondo, J. / Suzuki, C.
History
DepositionMar 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 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(P*UP*GP*CP*GP*UP*CP*GP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(P*UP*GP*CP*GP*UP*CP*GP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1376
Polymers14,7432
Non-polymers1,3944
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-107 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.429, 97.487, 47.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 7371.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H40N4O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, potassium chloride, G418, mercury(II) perchlorate

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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: Dec 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.81→48.74 Å / Num. obs: 6827 / % possible obs: 99.5 % / Redundancy: 3.522 % / Biso Wilson estimate: 38.895 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.117 / Χ2: 0.979 / Net I/σ(I): 9.86 / Num. measured all: 24046
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
2.81-2.893.4580.3323.7417055054930.9090.38997.6
2.89-2.963.6290.3044.3717534834830.9130.357100
2.96-3.053.6260.2235.5717914944940.9650.262100
3.05-3.143.5460.1526.8517024804800.9890.18100
3.14-3.253.5270.1228.1114854254210.990.14499.1
3.25-3.363.510.1248.615414414390.9860.14799.5
3.36-3.493.3590.1228.8914984474460.9890.14599.8
3.49-3.633.1670.19.9311973813780.990.1299.2
3.63-3.793.3050.1049.6713124043970.9890.12498.3
3.79-3.983.5340.09510.7313363783780.9940.112100
3.98-4.193.3010.08611.8811393463450.990.10399.7
4.19-4.453.6140.09911.9712183393370.9880.11699.4
4.45-4.753.8180.09212.9711953133130.9870.107100
4.75-5.133.8080.08113.6911312972970.9940.094100
5.13-5.623.7460.06415.0910192722720.9950.075100
5.62-6.293.6830.06815.29172492490.9930.079100
6.29-7.263.6490.06416.337372022020.9940.075100
7.26-8.893.5680.0617.146531831830.9940.07100
8.89-12.583.3620.05417.674741431410.9960.06498.6
12.58-48.743.0760.05618.1624380790.9920.06898.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k32

4k32


Resolution: 2.81→48.74 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 21.81 / Stereochemistry target values: ML
Details: The SF file contains friedel pairs under F_plus and F_minus columns.
RfactorNum. reflection% reflection
Rfree0.2287 666 9.78 %
Rwork0.1644 6146 -
obs0.1702 6812 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.83 Å2 / Biso mean: 30.5739 Å2 / Biso min: 12.79 Å2
Refinement stepCycle: final / Resolution: 2.81→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 920 70 11 1001
Biso mean--25.41 26.48 -
Num. residues----43
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 (%)
2.81-3.030.3711360.26031224136099
3.03-3.330.23551370.18591215135299
3.33-3.820.22991310.15561223135499
3.82-4.810.2211330.134612401373100
4.81-48.740.18241290.149812441373100

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