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- PDB-3fwo: The large ribosomal subunit from Deinococcus radiodurans complexe... -

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Basic information

Entry
Database: PDB / ID: 3fwo
TitleThe large ribosomal subunit from Deinococcus radiodurans complexed with Methymycin
Components
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
KeywordsRIBOSOME / large subunit / 50S / Deinococcus Radiodurans / X-ray structure / peptidyl-transferase / peptide bond formation / antibiotics / macrolides
Function / homologyChem-MT9 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.71 Å
AuthorsAuerbach, T. / Mermershtain, I. / Bashan, A. / Davidovich, C. / Rozenberg, H. / Sherman, D.H. / Yonath, A.
CitationJournal: Biotechnologia / Year: 2009
Title: Structural basis for the antibacterial activity of the 12-membered-ring mono-sugar macrolide methymycin
Authors: Auerbach, T. / Mermershtain, I. / Bashan, A. / Davidovich, C. / Rozenberg, H. / Sherman, D.H. / Yonath, A.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references / Structure summary
Revision 1.3Feb 21, 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: 23S RIBOSOMAL RNA
B: 5S RIBOSOMAL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)971,9043
Polymers971,4352
Non-polymers4701
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.499, 415.691, 701.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain 23S RIBOSOMAL RNA /


Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: GenBank: 6460405
#2: RNA chain 5S RIBOSOMAL RNA /


Mass: 38029.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Deinococcus radiodurans R1 (radioresistant)
References: GenBank: 6460405
#3: Chemical ChemComp-MT9 / (3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside / methymycin


Mass: 469.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H43NO7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 6.47 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: HEPES, NH4CL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-210.873
SYNCHROTRONESRF ID23-121
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 3152CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.8731
211
ReflectionResolution: 3.7→30 Å / Num. all: 266522 / Num. obs: 251032 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.167 / Net I/σ(I): 6.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.71→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 20427952.16 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.337 12496 5 %RANDOM
Rwork0.278 ---
obs0.278 251032 94.7 %-
all-266522 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.3087 Å2 / ksol: 0.2 e/Å3
Displacement parametersBiso mean: 134.2 Å2
Baniso -1Baniso -2Baniso -3
1--32.87 Å20 Å20 Å2
2--76.03 Å20 Å2
3----43.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.99 Å0.89 Å
Luzzati d res low-5 Å
Luzzati sigma a1.35 Å1.23 Å
Refinement stepCycle: LAST / Resolution: 3.71→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 61852 33 0 61885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramMETH_050808.top
X-RAY DIFFRACTION3ion.paramdna-rna-allatom.top
X-RAY DIFFRACTION4METH_050808.parion.top

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