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- PDB-3jq4: The structure of the complex of the large ribosomal subunit from ... -

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Basic information

Entry
Database: PDB / ID: 3jq4
TitleThe structure of the complex of the large ribosomal subunit from D. Radiodurans with the antibiotic lankacidin
Components
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRNA / Ribosome structure / antibiotics / lankacidin / lankamycin / protein synthesis / inhibitors / synergism / macrolide
Function / homologyChem-LC2 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.52 Å
AuthorsAuerbach-Nevo, T. / Mermershtain, I. / Davidovich, C. / Bashan, A. / Rozenberg, H. / Yonath, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics
Authors: Auerbach, T. / Mermershtain, I. / Davidovich, C. / Bashan, A. / Belousoff, M. / Wekselman, I. / Zimmerman, E. / Xiong, L. / Klepacki, D. / Arakawa, K. / Kinashi, H. / Mankin, A.S. / Yonath, A.
History
DepositionSep 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Structure summary
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)971,8943
Polymers971,4352
Non-polymers4601
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-21 kcal/mol
Surface area407440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.8, 410.3, 694.4
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 (radioresistant) / Strain: R1 / References: GenBank: 11612676
#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 (radioresistant) / Strain: R1 / References: GenBank: 11612676
#3: Chemical ChemComp-LC2 / N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide / Lankacidin C


Mass: 459.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H33NO7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: ETHANOL, DIMETHYL HEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.033201
SYNCHROTRONESRF ID23-220.873
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
MARMOSAIC 225 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0332011
20.8731
ReflectionResolution: 3.5→40 Å / Num. all: 293734 / Num. obs: 271411 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.163 / Net I/σ(I): 7.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
CCP4model building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NKW

1nkw


Resolution: 3.52→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 11982034.28 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): -2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.325 12314 5 %RANDOM
Rwork0.268 ---
obs0.268 248571 89.8 %-
all-276846 --
Solvent computationSolvent model: FLAT MODEL / Bsol: -12.7962 Å2 / ksol: 0.15 e/Å3
Displacement parametersBiso mean: 111.5 Å2
Baniso -1Baniso -2Baniso -3
1--32.14 Å20 Å20 Å2
2--81.81 Å20 Å2
3----49.67 Å2
Refinement stepCycle: LAST / Resolution: 3.52→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 61852 33 0 61885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramLAN_2007082nd_iter.top
X-RAY DIFFRACTION3ion.paramdna-rna-allatom.top
X-RAY DIFFRACTION4LAN_2007082nd_iter.parion.top

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