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- PDB-8jvs: Crystal structure of the chimeric protein tkoL2_v1 -

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Basic information

Entry
Database: PDB / ID: 8jvs
TitleCrystal structure of the chimeric protein tkoL2_v1
ComponentstkoL2_v1
KeywordsRIBOSOMAL PROTEIN / OB fold
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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


Theoretical massNumber of molelcules
Total (without water)5,9011
Polymers5,9011
Non-polymers00
Water91951
1
A: tkoL2_v1

A: tkoL2_v1


Theoretical massNumber of molelcules
Total (without water)11,8022
Polymers11,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1900 Å2
ΔGint-14 kcal/mol
Surface area5920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.509, 40.509, 68.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein tkoL2_v1


Mass: 5901.013 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.: 51 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2% PEG400, 100mM Tris pH8.5, 2000mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 17462 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.99 / Net I/σ(I): 13.17
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 2810 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.881 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 1759 10.08 %
Rwork0.1995 --
obs0.201 17449 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→34.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms384 0 0 51 435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007388
X-RAY DIFFRACTIONf_angle_d1.13522
X-RAY DIFFRACTIONf_dihedral_angle_d24.398154
X-RAY DIFFRACTIONf_chiral_restr0.6464
X-RAY DIFFRACTIONf_plane_restr0.00566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.54060.30311310.23941199X-RAY DIFFRACTION100
1.5406-1.58590.26721380.24151201X-RAY DIFFRACTION100
1.5859-1.63710.23381400.24081198X-RAY DIFFRACTION100
1.6371-1.69560.28321300.24021232X-RAY DIFFRACTION100
1.6956-1.76350.30461350.23951193X-RAY DIFFRACTION100
1.7635-1.84380.29551350.23951227X-RAY DIFFRACTION100
1.8438-1.9410.19871320.21891206X-RAY DIFFRACTION100
1.941-2.06260.21521330.20611200X-RAY DIFFRACTION100
2.0626-2.22180.17891390.19571215X-RAY DIFFRACTION100
2.2218-2.44540.20221360.19381183X-RAY DIFFRACTION100
2.4454-2.79910.26371400.21081212X-RAY DIFFRACTION100
2.7991-3.5260.20011360.19541206X-RAY DIFFRACTION100
3.526-34.8810.19261340.17951218X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.36521.8186-0.19768.7912-4.86534.1036-0.12430.2104-0.027-0.266-0.0464-0.26430.25020.2290.22530.24710.00010.02270.1892-0.0470.1885-7.29146.038.4161
24.08433.6923-2.28417.7151-4.77475.2964-0.02040.10150.25580.38910.15660.3784-0.1137-0.3083-0.21420.254-0.00450.01090.1929-0.04240.2421-13.48685.831714.2418
34.82981.98382.85933.14891.61638.0745-0.04450.2671-0.2791-0.13550.1293-0.2480.45330.5198-0.05260.20860.04160.02020.1952-0.03450.2309-3.60161.757411.724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 55 )

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