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- PDB-8jvu: Crystal structure of the chimeric protein tkoL2_v1.2 -

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Basic information

Entry
Database: PDB / ID: 8jvu
TitleCrystal structure of the chimeric protein tkoL2_v1.2
ComponentstkoL2_v1.2
KeywordsRIBOSOMAL PROTEIN / OB fold
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.505 Å
AuthorsYagi, S. / Tagami, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
Japan Society for the Promotion of Science (JSPS)20K15854 Japan
Japan Society for the Promotion of Science (JSPS)22H01346 Japan
CitationJournal: Nat Commun / Year: 2024
Title: An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins.
Authors: Yagi, S. / Tagami, S.
History
DepositionJun 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tkoL2_v1.2


Theoretical massNumber of molelcules
Total (without water)6,0051
Polymers6,0051
Non-polymers00
Water181
1
A: tkoL2_v1.2

A: tkoL2_v1.2


Theoretical massNumber of molelcules
Total (without water)12,0102
Polymers12,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Unit cell
Length a, b, c (Å)32.718, 32.718, 76.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein tkoL2_v1.2


Mass: 6005.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% 2-propanol, 100mM Tris-HCl pH8.5, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 3109 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.99 / Net I/σ(I): 12.74
Reflection shellResolution: 2.5→2.7 Å / Num. unique obs: 477 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.505→28.335 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 312 10.05 %
Rwork0.2446 --
obs0.247 3103 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.505→28.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms368 0 0 1 369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018373
X-RAY DIFFRACTIONf_angle_d2.106497
X-RAY DIFFRACTIONf_dihedral_angle_d30.212149
X-RAY DIFFRACTIONf_chiral_restr0.68859
X-RAY DIFFRACTIONf_plane_restr0.00860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.505-3.1550.37441520.37051379X-RAY DIFFRACTION100
3.155-28.3350.2431600.21721412X-RAY DIFFRACTION100

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