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- PDB-4f8v: Crystal structure of the bacterial ribosomal decoding site in com... -

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Basic information

Entry
Database: PDB / ID: 4f8v
TitleCrystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form)
ComponentsRNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA/ANTIBIOTIC / decording / ribosome / RNA-ANTIBIOTIC complex
Function / homologyChem-SIS / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKondo, J. / Koganei, M. / Kasahara, T.
CitationJournal: Acs Med.Chem.Lett. / Year: 2012
Title: Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site.
Authors: Kondo, J. / Koganei, M. / Kasahara, T.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Structure summary
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 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(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3814
Polymers13,4862
Non-polymers8952
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-16 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.650, 107.650, 48.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 6743.077 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin


Mass: 447.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H37N5O7 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na Cacodylate, Spermine, NaCl, MPD , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→44.5 Å / Num. obs: 4352

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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: 2.8→44.5 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.265 -10.1 %
Rwork0.226 --
obs-4352 97.1 %
Solvent computationBsol: 68.0444 Å2
Displacement parametersBiso max: 140.76 Å2 / Biso mean: 100.2348 Å2 / Biso min: 64.14 Å2
Baniso -1Baniso -2Baniso -3
1--12.742 Å20 Å20 Å2
2--41.071 Å20 Å2
3----28.33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 900 62 3 965
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.025
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.3682.5
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 (%)
2.8-2.90.5668470.543240044799.8
2.9-3.020.5097510.4957366417100
3.02-3.150.4066480.3835392440100
3.15-3.320.2818500.279137142197.7
3.32-3.530.3474390.270740544499.3
3.53-3.80.2728430.238537842196.3
3.8-4.180.2465480.245637442295
4.18-4.790.2507340.195639843297.5
4.79-6.030.2188480.167839744595.1
6.03-1000.2089430.180341746091.6
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1sis_xplor.param
X-RAY DIFFRACTION2dna-rna.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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