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- PDB-3bn0: The ribosomal protein S16 from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 3bn0
TitleThe ribosomal protein S16 from Aquifex aeolicus
Components30S ribosomal protein S16
KeywordsRIBOSOME / ribosomal protein / Ribonucleoprotein
Function / homology
Function and homology information


small ribosomal subunit / structural constituent of ribosome / translation / cytoplasm
Similarity search - Function
S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein bS16
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPylypenko, O. / Rak, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Extreme temperature tolerance of a hyperthermophilic protein coupled to residual structure in the unfolded state
Authors: Wallgren, M. / Aden, J. / Pylypenko, O. / Mikaelsson, T. / Johansson, L.B.-A. / Rak, A. / Wolf-Watz, M.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 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
A: 30S ribosomal protein S16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1602
Polymers13,0671
Non-polymers921
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.500, 54.500, 74.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

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Components

#1: Protein 30S ribosomal protein S16


Mass: 13067.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rpsP / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaTM 2 (DE3) / References: UniProt: O66523
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 2000 MME, 100mM Tris pH 6-7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97919 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 9015 / Num. obs: 9015 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.041 / Net I/σ(I): 17.55
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.71 / Rsym value: 0.197 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata scaling
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→8 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.011 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28787 445 5 %RANDOM
Rwork0.23845 ---
all0.24099 8461 --
obs0.24099 8461 100 %-
Displacement parametersBiso mean: 37.438 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms792 0 6 71 869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022840
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9661129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.805593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.83921.08137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91915166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.25159
X-RAY DIFFRACTIONr_chiral_restr0.1150.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02599
X-RAY DIFFRACTIONr_nbd_refined0.2130.2357
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.214
X-RAY DIFFRACTIONr_mcbond_it0.9941.5491
X-RAY DIFFRACTIONr_mcangle_it1.6482781
X-RAY DIFFRACTIONr_scbond_it1.9483405
X-RAY DIFFRACTIONr_scangle_it2.8824.5348
LS refinement shellResolution: 2.001→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 31 -
Rwork0.31 583 -
obs--100 %

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