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- PDB-8jvy: Crystal structure of the chimeric protein tkoL2_v1_turn with shor... -

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Basic information

Entry
Database: PDB / ID: 8jvy
TitleCrystal structure of the chimeric protein tkoL2_v1_turn with shorten loop 1
ComponentstkoL2_v1_turn
KeywordsRIBOSOMAL PROTEIN / OB fold
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 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_turn


Theoretical massNumber of molelcules
Total (without water)5,2391
Polymers5,2391
Non-polymers00
Water50428
1
A: tkoL2_v1_turn

A: tkoL2_v1_turn


Theoretical massNumber of molelcules
Total (without water)10,4792
Polymers10,4792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2530 Å2
ΔGint-19 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.825, 58.825, 54.465
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-124-

HOH

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Components

#1: Protein/peptide tkoL2_v1_turn


Mass: 5239.262 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.: 28 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 200mM Ammonium citrate tribasic pH7.5

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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: 1.895→50 Å / Num. obs: 8373 / % possible obs: 99.7 % / Redundancy: 10.3 % / CC1/2: 1 / Net I/σ(I): 32.58
Reflection shellResolution: 1.895→2 Å / Num. unique obs: 1344 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.895→37.205 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 842 10.06 %
Rwork0.2256 --
obs0.2276 8371 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.895→37.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms367 0 0 28 395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012375
X-RAY DIFFRACTIONf_angle_d1.329505
X-RAY DIFFRACTIONf_dihedral_angle_d25.949151
X-RAY DIFFRACTIONf_chiral_restr0.93462
X-RAY DIFFRACTIONf_plane_restr0.00464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.895-2.01340.41661450.35661249X-RAY DIFFRACTION99
2.0134-2.16880.31941350.28911265X-RAY DIFFRACTION100
2.1688-2.3870.3531380.2751229X-RAY DIFFRACTION100
2.387-2.73240.29261400.25741258X-RAY DIFFRACTION100
2.7324-3.44210.24881400.22191261X-RAY DIFFRACTION100
3.4421-37.2050.18911440.1861267X-RAY DIFFRACTION100

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