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- PDB-7edl: Crystal structure of the bacterial ribosomal decoding site in com... -

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Basic information

Entry
Database: PDB / ID: 7edl
TitleCrystal structure of the bacterial ribosomal decoding site in complex with G418 and Hg(II)
ComponentsRNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*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: 2.6 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 prokaryotic 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*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1356
Polymers14,7412
Non-polymers1,3944
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-102 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.640, 97.301, 47.060
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*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')


Mass: 7370.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, sodium chloride, spermine tetrahydrochloride, 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: 2.6→48.65 Å / Num. obs: 8525 / % possible obs: 99.3 % / Redundancy: 3.516 % / Biso Wilson estimate: 50.008 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.065 / Χ2: 1.04 / Net I/σ(I): 15.16
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
2.61-2.673.5930.3363.4222676366310.9080.39599.2
2.67-2.753.6150.2514.2821586015970.9460.29499.3
2.75-2.833.6050.1766.0822106186130.9770.20799.2
2.83-2.913.5190.1676.5420415825800.9690.19799.7
2.91-3.013.4780.1328.7719585665630.9770.15599.5
3.01-3.113.3610.07612.1618725585570.9950.0999.8
3.11-3.233.1340.05913.4916145215150.9970.07198.8
3.23-3.363.2350.05316.3416245055020.9970.06499.4
3.36-3.513.5470.0617.0418165135120.9950.07199.8
3.51-3.683.3290.04818.3514684454410.9970.05899.1
3.68-3.883.5290.04818.8415954564520.9980.05799.1
3.88-4.123.8320.04522.5415524084050.9970.05399.3
4.12-4.43.7610.04823.6214974013980.9970.05699.3
4.4-4.763.6980.04525.113243593580.9970.05399.7
4.76-5.213.6790.04724.8312733473460.9970.05599.7
5.21-5.833.6280.04226.4210522942900.9970.04998.6
5.83-6.733.5460.04125.619612742710.9960.04798.9
6.73-8.243.5630.03728.118162342290.9980.04397.9
8.24-11.653.3780.03728.55811731720.9970.04399.4
11.65-48.653.140.0329.5429297930.9980.03595.9

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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: 2.6→48.65 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.68 / Stereochemistry target values: ML
Details: The SF file contains friedel pairs under F_plus and F_minus columns.
RfactorNum. reflection% reflection
Rfree0.2216 851 9.99 %
Rwork0.1863 7666 -
obs0.1899 8517 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.74 Å2 / Biso mean: 40.6951 Å2 / Biso min: 22.24 Å2
Refinement stepCycle: final / Resolution: 2.6→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 920 70 20 1010
Biso mean--36.71 37.13 -
Num. residues----43
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6-2.770.43941400.35131278
2.77-2.980.30631400.27491271
2.98-3.280.2481480.21681273
3.28-3.760.17461400.16731288
3.76-4.720.19311410.15081282
4.73-48.650.19191420.151274

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