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- PDB-3bnl: Crystal structure of the bacterial ribosomal decoding A site in t... -

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Basic information

Entry
Database: PDB / ID: 3bnl
TitleCrystal structure of the bacterial ribosomal decoding A site in the presence of [Co(NH3)6]Cl3
ComponentsA site of bacterial ribosome
KeywordsRNA / ribosome / decoding site
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.602 Å
AuthorsKondo, J. / Westhof, E.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates
Authors: Kondo, J. / Westhof, E.
History
DepositionDec 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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

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Assembly

Deposited unit
A: A site of bacterial ribosome
B: A site of bacterial ribosome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,38710
Polymers14,0982
Non-polymers1,2898
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.599, 73.599, 63.496
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: RNA chain A site of bacterial ribosome


Mass: 7049.243 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium cacodylate, KCl, 2-methyl-2,4-pentanediol, spermine tetrachloride, hexammine cobalt chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2KCl11
3Sodium cacodylate11
4[Co(NH3)6]Cl311
5MPD12
6KCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.91636 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91636 Å / Relative weight: 1
ReflectionResolution: 2.602→36.8 Å / Num. obs: 5295 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.602-2.747.30.2862.657247800.286100
2.74-2.917.30.1445.152837220.144100
2.91-3.117.30.0739.449276750.073100
3.11-3.367.30.04912.547116490.049100
3.36-3.687.20.04314.541495730.043100
3.68-4.117.10.04413.537875310.044100
4.11-4.7570.05411.133044710.054100
4.75-5.816.70.04413.326844010.044100
5.81-8.226.60.03313.220623130.033100
8.22-36.86.20.0489.811161800.04898.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.602→36 Å / FOM work R set: 0.811 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.251 556 10.5 %
Rwork0.22 --
obs-5278 99.7 %
Solvent computationBsol: 181.362 Å2
Displacement parametersBiso mean: 44.093 Å2
Baniso -1Baniso -2Baniso -3
1--1.711 Å20 Å20 Å2
2---1.711 Å20 Å2
3---3.423 Å2
Refinement stepCycle: LAST / Resolution: 2.602→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 940 56 38 1034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION2nco_xplor.paramnco_xplor.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

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