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- PDB-1ffz: LARGE RIBOSOMAL SUBUNIT COMPLEXED WITH R(CC)-DA-PUROMYCIN -

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Basic information

Entry
Database: PDB / ID: 1ffz
TitleLARGE RIBOSOMAL SUBUNIT COMPLEXED WITH R(CC)-DA-PUROMYCIN
Components
  • 23S RIBOSOMAL RNA
  • R(P*CP*C*)-D(P*A)-R(P*(PU))
KeywordsRIBOSOME / ribosome assembly / RNA-RNA complex / Ribozyme / ribosomal RNA
Function / homology: / DNA/RNA hybrid / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsNissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.A.
Citation
Journal: Science / Year: 2000
Title: The structural basis of ribosome activity in peptide bond synthesis.
Authors: Nissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.A.
#1: Journal: Science / Year: 2000
Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
Authors: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A.
#2: Journal: Nature / Year: 1999
Title: Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit
Authors: Ban, N. / Nissen, P. / Hansen, J. / Capel, M. / Moore, P.B. / Steitz, T.A.
#3: Journal: Biochemistry / Year: 1995
Title: An inhibitor of ribosomal peptidyl transferase using transition-state analogy
Authors: Welch, M. / Chastang, J. / Yarus, M.
History
DepositionJul 26, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S RIBOSOMAL RNA
B: R(P*CP*C*)-D(P*A)-R(P*(PU))


Theoretical massNumber of molelcules
Total (without water)196,2642
Polymers196,2642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.000, 300.000, 574.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: RNA chain 23S RIBOSOMAL RNA


Mass: 194851.688 Da / Num. of mol.: 1 / Fragment: DOMAIN V OF 23S RIBOSOMAL RNA / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779
#2: DNA/RNA hybrid R(P*CP*C*)-D(P*A)-R(P*(PU))


Mass: 1412.087 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: AN ANALOG OF A-SITE AMINOACYL-TRNA AND P-SITE PEPTIDYL-TRNA AS THEY ARE COVALENTLY LINKED BY THE TETRAHEDRAL CARBONYL CARBON INTERMEDIATE IN PEPTIDE BOND FORMATION. CONTAINS PU, PUROMYCIN-N-AMINOPHOSPHONIC ACID

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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

Crystal growTemperature: 292 K / Method: back-extraction, vapor diffusion / pH: 5.8
Details: PEG 6000, KCl, NH4Cl, potassium acetate, MgCl2, CdCl2, Tris-MES. Complex obtained by crystal soaking in 0.1 mM rCC-dA-p-Puromycin, pH 5.8, Back-extraction, vapor diffusion, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2NH4Cl11
3MgCl211
4CdCl211
5potassium acetate11
6Tris-MES11
7PEG 600011
8PEG 600012
Crystal grow
*PLUS
pH: 7.1 / Method: unknown / Details: Ban, N., (2000) Science, 289, 905.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
11.2 M1KCl
20.5 M1NH4Cl
3100 mMKacetate1
430 mM1MgCl2
57 %PEG60001
615 mMTris1
715 mMMES1
81 mM1CdCl21

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→70 Å / Num. all: 367284 / Num. obs: 367284 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.188 / Net I/σ(I): 11
Reflection shellResolution: 3.17→3.23 Å / Redundancy: 6 % / Rmerge(I) obs: 0.84 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 2590726
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
Omodel building
CNSphasing
RefinementResolution: 3.2→70 Å / Num. reflection all: 367284 / Num. reflection obs: 367284 / σ(F): 0 / σ(I): 0
Details: The structure has been obtained by fitting to the experimental map. No refinement has been performed at this stage
Refinement stepCycle: LAST / Resolution: 3.2→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 10725 0 0 10725
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 70 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS

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