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- PDB-4pdq: Crystal structure of the bacterial ribosomal decoding site in com... -

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Basic information

Entry
Database: PDB / ID: 4pdq
TitleCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog
ComponentsRNA (5'-*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/ANTIBIOTIC / ribosome / aminoglycoside / RNA-ANTIBIOTIC complex
Function / homologyChem-NMZ / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsHanessian, S. / Saavedra, O.M. / Vilchis-Reyes, M.A. / Maianti, J.P. / Kanazawa, H. / Dozzo, P. / Feeney, L.A. / Armstrong, E.S. / Kondo, J.
CitationJournal: Chem Sci / Year: 2014
Title: Synthesis, broad spectrum antibacterial activity, and X-ray co-crystal structure of the decoding bacterial ribosomal A-site with 4'-deoxy-4'-fluoro neomycin analogs
Authors: Hanessian, S. / Saavedra, O.M. / Vilchis-Reyes, M.A. / Maianti, J.P. / Kanazawa, H. / Dozzo, P. / Matias, R.D. / Serio, A. / Kondo, J.
History
DepositionApr 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-*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'-*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)15,5075
Polymers14,7412
Non-polymers7663
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-21 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.657, 103.657, 44.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: RNA chain RNA (5'-*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 (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NMZ / (2S)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-3-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy }-4-[(2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranosyl)oxy]-2-hydroxycyclohexyl}-2-hydroxybutanamide / 1-N-[(S)-4-Amino-2-hydroxybutanoyl]-4'-deoxy-4'-fluoro-4'-epineomycin


Mass: 717.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H52FN7O14
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium cacodylate, MgCl2, MPD, Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→19.6 Å / Num. obs: 3522 / % possible obs: 98.7 % / Redundancy: 5.6 % / Net I/σ(I): 12.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIXphasing
PHENIXmodel building
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.6 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.236 355 9.9 %
Rwork0.195 --
obs0.195 3522 98.4 %
Solvent computationBsol: 59.88 Å2
Displacement parametersBiso mean: 76.3504 Å2
Baniso -1Baniso -2Baniso -3
1-1.052 Å20 Å20 Å2
2--1.052 Å20 Å2
3----2.104 Å2
Refinement stepCycle: LAST / Resolution: 3→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 974 51 1 1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.6922
X-RAY DIFFRACTIONc_scangle_it2.7222.5
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection% reflection
Rfree0.301 37 -
Rwork0.3192 322 -
obs--100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1DNA-RNA_FREE.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION4GET_XPLOR.PARAM
X-RAY DIFFRACTION5174.PARAM

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