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- PDB-9f9u: Crystal structure of Saccharolobus solfataricus NusA2 -

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Basic information

Entry
Database: PDB / ID: 9f9u
TitleCrystal structure of Saccharolobus solfataricus NusA2
ComponentsTranscription elongation factor NusA
KeywordsRNA BINDING PROTEIN / crenarchaea / zinc-finger protein / alpha-beta fold / RNA-binding protein
Function / homologyTranscription elongation factor NusA
Function and homology information
Biological speciesSaccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsPilottto, S. / Phung, D.K. / Werner, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust207446/Z/17/Z United Kingdom
CitationJournal: Structure / Year: 2025
Title: Archaeal NusA2 is the ancestor of ribosomal protein eS7 in eukaryotes.
Authors: Phung, D.K. / Pilotto, S. / Matelska, D. / Blombach, F. / Pinotsis, N. / Hovan, L. / Gervasio, F.L. / Werner, F.
History
DepositionMay 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation factor NusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6322
Polymers19,5671
Non-polymers651
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.467, 72.813, 41.746
Angle α, β, γ (deg.)90.000, 111.950, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Transcription elongation factor NusA


Mass: 19566.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Strain: P2 / Gene: SSO0172 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q980V4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% w/v PEG 20,000, 2% v/v 1,4-dioxane, 100 mM Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2826 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.68→72.88 Å / Num. obs: 21422 / % possible obs: 95.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 16.6
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 1.086 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1683 / CC1/2: 0.462 / Rpim(I) all: 0.493 / Rrim(I) all: 1.199 / % possible all: 75.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXDEphasing
ARP/wARPmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SAD / Resolution: 1.68→38.72 Å / SU ML: 0.2556 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 31.3196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 950 4.63 %
Rwork0.2164 19557 -
obs0.2173 20507 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.53 Å2
Refinement stepCycle: LAST / Resolution: 1.68→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 1 141 1512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841412
X-RAY DIFFRACTIONf_angle_d1.01211912
X-RAY DIFFRACTIONf_chiral_restr0.0622232
X-RAY DIFFRACTIONf_plane_restr0.0093238
X-RAY DIFFRACTIONf_dihedral_angle_d5.2477195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.770.39241070.32462041X-RAY DIFFRACTION67.48
1.77-1.880.33931230.29772627X-RAY DIFFRACTION86.13
1.88-2.020.34081230.27172780X-RAY DIFFRACTION91.12
2.02-2.230.27231480.21582951X-RAY DIFFRACTION96.63
2.23-2.550.27511480.22893010X-RAY DIFFRACTION98.26
2.55-3.210.23961350.22413069X-RAY DIFFRACTION99.53
3.21-38.720.19351660.18953079X-RAY DIFFRACTION99.94

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