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- PDB-7edn: Crystal structure of the eukaryotic decoding site in complex with... -

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Basic information

Entry
Database: PDB / ID: 7edn
TitleCrystal structure of the eukaryotic decoding site in complex with Ag(I)
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 / Silver / Decoding site / Ribosomal RNA
Function / homologySILVER ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 decoding site in complex with Ag(I)
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6274
Polymers7,3711
Non-polymers2563
Water00
1
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')
hetero molecules

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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2548
Polymers14,7432
Non-polymers5126
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_955-x+4,y,-z1
Unit cell
Length a, b, c (Å)51.176, 28.102, 37.711
Angle α, β, γ (deg.)90.000, 102.350, 90.000
Int Tables number5
Space group name H-MC121

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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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
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: 1.8 Å3/Da / Density % sol: 31.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MOPS, MPD, spermine, calcium nitrate, silver nitrate, G418

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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: 2.6→36.84 Å / Num. obs: 3135 / % possible obs: 99.2 % / Redundancy: 3.374 % / Biso Wilson estimate: 64.023 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.128 / Χ2: 1.053 / Net I/σ(I): 6.88 / Num. measured all: 10577
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.683.3920.3282.492680.9410.38998.2
2.68-2.773.480.3252.692540.9250.385100
2.77-2.863.4530.2553.552670.9390.302100
2.86-2.973.4320.1274.692360.9960.15197.1
2.97-3.093.2660.1385.472480.9830.167100
3.09-3.232.9690.1337.052260.9760.1799.6
3.23-3.393.1020.1156.842150.9870.14296.8
3.39-3.573.1940.1347.812060.9740.162100
3.57-3.793.1720.1218.171920.9780.14996.5
3.79-4.053.4610.1089.861910.9920.128100
4.05-4.383.6870.09610.291630.990.11198.8
4.38-4.793.5490.09610.191750.9840.113100
4.79-5.363.6420.11210.371340.9680.13297.1
5.36-6.193.6620.110.611300.9770.118100
6.19-7.583.4290.08110.541050.9850.097100
7.58-10.723.5620.10510.92800.980.12398.8
10.72-36.843.2220.08410.53450.9790.10295.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3td0

3td0


Resolution: 2.6→36.84 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 34.11 / Stereochemistry target values: ML
Details: The SF file contains friedel pairs under F_plus and F_minus columns.
RfactorNum. reflection% reflection
Rfree0.2518 308 9.95 %
Rwork0.1877 2787 -
obs0.1939 3095 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.13 Å2 / Biso mean: 70.2578 Å2 / Biso min: 35.19 Å2
Refinement stepCycle: final / Resolution: 2.6→36.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 470 3 0 473
Biso mean--83.51 --
Num. residues----22
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-3.270.34121560.247613821538
3.28-36.840.22671520.171514051557

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