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- PDB-5z1h: Crystal structure of the bacterial ribosomal decoding site in com... -

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Basic information

Entry
Database: PDB / ID: 5z1h
TitleCrystal structure of the bacterial ribosomal decoding site in complex with 6'-fluoro sisomicin
ComponentsRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / rRNA / aminoglycoside
Function / homologyChem-FSJ / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsKanazawa, H. / Hanessian, S. / Kondo, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K08248 Japan
CitationJournal: ChemMedChem / Year: 2018
Title: Structure-Based Design of a Eukaryote-Selective Antiprotozoal Fluorinated Aminoglycoside.
Authors: Kanazawa, H. / Saavedra, O.M. / Maianti, J.P. / Young, S.A. / Izquierdo, L. / Smith, T.K. / Hanessian, S. / Kondo, J.
History
DepositionDec 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*UP*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(*UP*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)15,1913
Polymers14,7412
Non-polymers4511
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-17 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.905, 31.665, 46.696
Angle α, β, γ (deg.)90.000, 94.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (5'-R(*UP*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-FSJ / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(fluoromethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / 6'-fluoro sisomicin


Mass: 450.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H35FN4O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2-Methyl-2,4-pentanediol, LiCl, spermine tetrahydrochloride, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→42.8 Å / Num. obs: 5052 / % possible obs: 99.7 % / Redundancy: 3.54 % / Biso Wilson estimate: 39.59 Å2 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.084 / Χ2: 0.92 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
2.4-2.493.610.2723.24860.91100
2.49-2.593.620.2623.15110.91100
2.59-2.73.590.2273.45040.82100
2.7-2.853.610.1764.45000.87100
2.85-3.023.60.1275.74970.84100
3.02-3.263.530.1029.35041.0799.8
3.26-3.583.540.06911.85120.9699.8
3.58-4.13.530.06713.14990.89100
4.1-5.173.50.0614.45160.8699.6
5.17-42.753.290.05716.55231.0898.1

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Processing

Software
NameVersionClassification
d*TREK9.4SSIdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 2.4→42.8 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.44
RfactorNum. reflection% reflection
Rfree0.2632 495 9.81 %
Rwork0.2125 --
obs0.2171 5047 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 241.24 Å2 / Biso mean: 41.16 Å2 / Biso min: 14.91 Å2
Refinement stepCycle: final / Resolution: 2.4→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 893 31 87 1011
Biso mean--26.81 38.59 -
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071027
X-RAY DIFFRACTIONf_angle_d1.0081593
X-RAY DIFFRACTIONf_chiral_restr0.097220
X-RAY DIFFRACTIONf_plane_restr0.0242
X-RAY DIFFRACTIONf_dihedral_angle_d11.549496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.64160.34211250.292211331258100
2.6416-3.02370.3231320.273711081240100
3.0237-3.80920.25441250.190311361261100
3.8092-42.76030.21731130.18811175128899

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