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- PDB-8a8s: 30S ribosomal protein S24e from Thermococcus kodakarensis -

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Basic information

Entry
Database: PDB / ID: 8a8s
Title30S ribosomal protein S24e from Thermococcus kodakarensis
Components30S ribosomal protein S24e
KeywordsGENE REGULATION / high pressure adaptation protein dynamics structural constituent of ribosome
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex
Similarity search - Function
Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Small ribosomal subunit protein eS24
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.659 Å
AuthorsCalio, A. / Hoh, F.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)17-CE11-0012-01 France
Centre National de la Recherche Scientifique (CNRS)MITI OriginsUnderPressure et LifeAdapt France
CitationJournal: To Be Published
Title: 30S ribosomal protein S24e from Thermococcus kodakarensis
Authors: Calio, A. / Hoh, F.
History
DepositionJun 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S ribosomal protein S24e


Theoretical massNumber of molelcules
Total (without water)11,2001
Polymers11,2001
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.551, 55.272, 37.579
Angle α, β, γ (deg.)90.000, 98.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 30S ribosomal protein S24e


Mass: 11199.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: rps24e, TK1696 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIY8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0,1M sodium acetate pH 4,6 30% PEG 300 / PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.69 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.69 Å / Relative weight: 1
ReflectionResolution: 1.659→37.1 Å / Num. obs: 9962 / % possible obs: 88 % / Redundancy: 1.6 % / CC1/2: 0.997 / Net I/σ(I): 10.5
Reflection shellResolution: 1.659→1.687 Å / Rmerge(I) obs: 0.32 / Num. unique obs: 453 / CC1/2: 0.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS2020417data reduction
Aimless0.74data scaling
PHASERphasing
PHENIXV1.20.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V94

2v94


Resolution: 1.659→30.81 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.26 --
Rwork0.22 --
obs-9956 88 %
Displacement parametersBiso max: 58.93 Å2 / Biso mean: 22.696 Å2 / Biso min: 9.7 Å2
Refinement stepCycle: LAST / Resolution: 1.659→30.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms785 0 0 82 867

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