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- PDB-4pdb: CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN C... -

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Basic information

Entry
Database: PDB / ID: 4pdb
TitleCRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN COMPLEX WITH AN RNA APTAMER
Components
  • 30S ribosomal protein S8
  • SELEX RNA aptamer
KeywordsRIBOSOMAL PROTEIN/RNA / PROTEIN-RNA COMPLEX SELEX BASE TRIPLE TRANSLATION / RIBOSOMAL PROTEIN-RNA complex
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #30 / Dna Ligase; domain 1 - #10 / Ribosomal Protein S8; Chain: A, domain 1 / Dna Ligase; domain 1 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Ribosomal protein S8 signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / 30S ribosomal protein S8 / :
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDavlieva, M. / Shamoo, Y. / Nikonowicz, E.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1 AI080714 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM73969 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI057156 United States
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis.
Authors: Davlieva, M. / Donarski, J. / Wang, J. / Shamoo, Y. / Nikonowicz, E.P.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 30S ribosomal protein S8
I: SELEX RNA aptamer


Theoretical massNumber of molelcules
Total (without water)29,5762
Polymers29,5762
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-17 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.410, 59.270, 92.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 30S ribosomal protein S8 /


Mass: 17367.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: rpsH / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: W0CSD8, UniProt: Q81VR6*PLUS
#2: RNA chain SELEX RNA aptamer


Mass: 12209.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 M di-ammonium hydrogen citrate, 100 mM sodium chloride, 16% PEG 3350, 10 mM spermidine

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.976 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 31, 2009
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 9801 / Num. obs: 9796 / % possible obs: 99.9 % / Redundancy: 7.08 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.73 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
REFMAC5.7.0032refinement
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.215 Å / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 1.37 / ESU R: 0.121 / ESU R Free: 0.069 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 471 4.81 %Random
Rwork0.189 ---
obs0.1922 9325 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.43 Å2
Baniso -1Baniso -2Baniso -3
1--13.52 Å20 Å20 Å2
2--6.95 Å20 Å2
3---6.57 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 810 0 17 1848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081937
X-RAY DIFFRACTIONf_angle_d1.262796
X-RAY DIFFRACTIONf_dihedral_angle_d17.174859
X-RAY DIFFRACTIONf_chiral_restr0.051350
X-RAY DIFFRACTIONf_plane_restr0.005216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.599-2.6660.2231630.15443211X-RAY DIFFRACTION100
2.6002-2.97610.37841480.28283049X-RAY DIFFRACTION100
2.9761-3.74820.29511600.21713059X-RAY DIFFRACTION100

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