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- PDB-5zem: Crystal structure of the bacterial A1408me1A-mutant ribosomal dec... -

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Basic information

Entry
Database: PDB / ID: 5zem
TitleCrystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in the presence of gentamicin
ComponentsRNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / ribosome / aminoglycoside / antibiotic-resistance
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.103 Å
AuthorsKanazawa, H. / Baba, F. / Koganei, M. / Kondo, J.
Funding support Japan, 7items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)23790054 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)26860025 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K08248 Japan
Kurata Grant2013- 20 Japan
Ichiro Kanehara Foundation15KI192 Japan
Japan Science Society28-325 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K08248 Japan
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Authors: Kanazawa, H. / Baba, F. / Koganei, M. / Kondo, J.
History
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 21, 2018ID: 4WCS
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*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*(1MA)P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)14,1272
Polymers14,1272
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-5 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.584, 91.995, 47.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

21A-111-

HOH

31A-112-

HOH

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Components

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


Mass: 7063.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium cacodylate, spermine, MPD, Potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→42.3 Å / Num. obs: 2851 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13
Reflection shellResolution: 3.1→3.2 Å / Rmerge(I) obs: 0.284

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.22data extraction
PHENIXphasing
CrystalCleardata scaling
Cootmodel building
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TD1

3td1


Resolution: 3.103→42.3 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 35.87
RfactorNum. reflection% reflection
Rfree0.2835 261 9.39 %
Rwork0.2552 --
obs0.258 2780 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 258.83 Å2 / Biso mean: 107.83 Å2 / Biso min: 75.21 Å2
Refinement stepCycle: final / Resolution: 3.103→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 920 0 19 939
Biso mean---125.99 -
Num. residues----43
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071026
X-RAY DIFFRACTIONf_angle_d1.1431596
X-RAY DIFFRACTIONf_chiral_restr0.06213
X-RAY DIFFRACTIONf_plane_restr0.00643
X-RAY DIFFRACTIONf_dihedral_angle_d16.735498
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.20.30531180.31711200131895
3.9089-42.34620.27871430.24161319146299

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