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- PDB-4gpx: Crystal structure of the protozoal cytoplasmic ribosomal decoding... -

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Basic information

Entry
Database: PDB / ID: 4gpx
TitleCrystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form)
ComponentsRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA/ANTIBIOTIC / ribosome / aminoglycoside / RNA-ANTIBIOTIC complex / antiprotozoal activity / antibacterial activity
Function / homologyChem-6HS / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKondo, J. / Koganei, M. / Maianti, J.P. / Ly, V.L. / Hanessian, S.
CitationJournal: Chemmedchem / Year: 2013
Title: Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites
Authors: Kondo, J. / Koganei, M. / Maianti, J.P. / Ly, V.L. / Hanessian, S.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*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*GP*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)15,6704
Polymers14,7732
Non-polymers8972
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-15 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 51.623, 58.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 7386.424 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-6HS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / 6'-hydroxysisomicin


Mass: 448.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H36N4O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na Cacodylate, Spermine, NaCl, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 210 / Detector: CCD / Date: Jun 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→36.8 Å / Num. obs: 4696

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
CNS1.3refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→36.8 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.252 492 10.4 %
Rwork0.223 --
obs-4695 99.1 %
Solvent computationBsol: 37.9883 Å2
Displacement parametersBiso max: 104.2 Å2 / Biso mean: 67.4001 Å2 / Biso min: 34.75 Å2
Baniso -1Baniso -2Baniso -3
1-27.418 Å20 Å20 Å2
2--3.896 Å20 Å2
3----31.314 Å2
Refinement stepCycle: LAST / Resolution: 2.6→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 902 62 11 975
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d0.894
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.4952
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.2392.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.690.427590.4543409468100
2.69-2.80.4502480.479410458100
2.8-2.930.516450.4001417462100
2.93-3.080.382440.3388406450100
3.08-3.280.3231420.254643347599.8
3.28-3.530.3485500.2508412462100
3.53-3.880.2366490.2066425474100
3.88-4.450.1661510.1847426477100
4.45-5.60.2257560.1719429485100
5.6-1000.1842480.162243648492.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4115_xplor.param

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