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- PDB-1k01: Structural Basis for the Interaction of Antibiotics with the Pept... -

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Basic information

Entry
Database: PDB / ID: 1k01
TitleStructural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria
Components
  • (Ribosomal Protein ...) x 3
  • 23S rRNA23S ribosomal RNA
KeywordsRIBOSOME / 50S / 23S / 5S / Antibiotics / Chloramphenicol / Peptidyl transferase center
Function / homology
Function and homology information


large ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / metal ion binding
Similarity search - Function
Ribosomal protein L32p, bacterial type / Ribosomal protein L22, bacterial/chloroplast-type / : / Ribosomal L32p protein family / Ribosomal protein L32p / 50S ribosomal protein uL4 / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily ...Ribosomal protein L32p, bacterial type / Ribosomal protein L22, bacterial/chloroplast-type / : / Ribosomal L32p protein family / Ribosomal protein L32p / 50S ribosomal protein uL4 / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L4/L1 family / Zinc-binding ribosomal protein
Similarity search - Domain/homology
CHLORAMPHENICOL / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL4
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.5 Å
AuthorsSchluenzen, F. / Zarivach, R. / Harms, J. / Bashan, A. / Tocilj, A. / Albrecht, R. / Yonath, A. / Franceschi, F.
CitationJournal: Nature / Year: 2001
Title: Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria.
Authors: Schlunzen, F. / Zarivach, R. / Harms, J. / Bashan, A. / Tocilj, A. / Albrecht, R. / Yonath, A. / Franceschi, F.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 rRNA
K: Ribosomal Protein L4
L: Ribosomal Protein L22
M: Ribosomal Protein L32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)978,1108
Polymers977,7144
Non-polymers3964
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.100, 409.300, 696.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 23S rRNA / 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: 15805042

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Ribosomal Protein ... , 3 types, 3 molecules KLM

#2: Protein Ribosomal Protein L4 / 60S ribosomal protein L4 / Coordinate model: Cα atoms only


Mass: 22308.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXK1
#3: Protein Ribosomal Protein L22 / 60S ribosomal protein L22 / Coordinate model: Cα atoms only


Mass: 15190.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ7
#4: Protein Ribosomal Protein L32 / / 50S ribosomal protein L32 / Coordinate model: Cα atoms only


Mass: 6810.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: P49228

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CLM / CHLORAMPHENICOL / Chloramphenicol


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM

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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: 4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1ethanol11
2dimethylhexanediol11
3MgCl211
4KCl11
5Hepes11
6NH4Cl11
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mM1reservoirMgCl2
260 mM1reservoirNH4Cl
35 mM1reservoirKCl
410 mMHEPES1reservoir
51
61

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2001
RadiationMonochromator: Si111 or Si311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.5→25 Å / Num. all: 238661 / Num. obs: 238661 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.5→3.62 Å / % possible all: 71
Reflection
*PLUS
Lowest resolution: 25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.124
Reflection shell
*PLUS
% possible obs: 71 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.5→30 Å / σ(F): 0
Details: The coordinates of four chains of the 50s subunit and chloramphenicol were deposited. The number of non-hydrogen atoms used in refinement is more than specified in REMARK 3: 26069 protein ...Details: The coordinates of four chains of the 50s subunit and chloramphenicol were deposited. The number of non-hydrogen atoms used in refinement is more than specified in REMARK 3: 26069 protein atoms, 62115 nucleic acid atoms, and 102 heterogen atoms were used in refinement.
RfactorNum. reflectionSelection details
Rfree0.321 11455 Random
Rwork0.275 --
all0.281 238661 -
obs0.281 238661 -
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms385 59532 23 0 59940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.67
Software
*PLUS
Name: CNS/REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS

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