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- PDB-1z58: Crystal structure of a complex of the ribosome large subunit with... -

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Basic information

Entry
Database: PDB / ID: 1z58
TitleCrystal structure of a complex of the ribosome large subunit with rapamycin
Components23S RIBOSOMAL RNA
KeywordsRIBOSOME / tunnel / polyketyde
Function / homologyRAPAMYCIN IMMUNOSUPPRESSANT DRUG / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsAmit, M. / Berisio, R. / Baram, D. / Harms, J. / Bashan, A. / Yonath, A.
CitationJournal: Febs Lett. / Year: 2005
Title: A crevice adjoining the ribosome tunnel: Hints for cotranslational folding.
Authors: Amit, M. / Berisio, R. / Baram, D. / Harms, J. / Bashan, A. / Yonath, A.
History
DepositionMar 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
2: 23S RIBOSOMAL RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)934,3192
Polymers933,4051
Non-polymers9141
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.500, 404.000, 689.000
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) / References: GenBank: 6460050
#2: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Sirolimus


Mass: 914.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H79NO13 / Comment: immunosuppressant, antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.6 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7
Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7, EVAPORATION, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1ETHANOL11
2DIMETHYLHEXANEDIOL11
3MGCL211
4KCL11
5HEPES11
6NH4CL11
7H2O11
8MGCL212
9KCL12
10NH4CL12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.93
SYNCHROTRONESRF ID14-420.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 191012 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 6.06
Reflection shellResolution: 3.8→3.94 Å / % possible all: 74.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.368 9550 RANDOM
Rwork0.273 --
all0.304 --
obs0.304 191012 -
Refine analyze
FreeObs
Luzzati coordinate error0.05 Å0.04 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 3.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 59359 65 0 59424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.61
LS refinement shellResolution: 3.8→3.94 Å / Rfactor Rfree: 0.368 / Rfactor Rwork: 0.273

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