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- PDB-8jvw: Crystal structure of the dimeric DZBB fold protein tkoL2_v1.2_Z -

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Basic information

Entry
Database: PDB / ID: 8jvw
TitleCrystal structure of the dimeric DZBB fold protein tkoL2_v1.2_Z
ComponentstkoL2_v1.2_Z
KeywordsDNA BINDING PROTEIN / Double zeta beta barrel
Function / homologyGLYCINE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.806 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_Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7654
Polymers4,5391
Non-polymers2253
Water45025
1
A: tkoL2_v1.2_Z
hetero molecules

A: tkoL2_v1.2_Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5298
Polymers9,0792
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3310 Å2
ΔGint-24 kcal/mol
Surface area4940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.959, 44.427, 84.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

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Components

#1: Protein/peptide tkoL2_v1.2_Z


Mass: 4539.474 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: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 70% MPD, 100mM HEPES pH7.0

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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: 1.8→50 Å / Num. obs: 7929 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.99 / Net I/σ(I): 18.77
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 1257 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.806→42.145 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 789 9.96 %
Rwork0.2106 --
obs0.2128 7920 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.806→42.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms288 0 15 25 328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024301
X-RAY DIFFRACTIONf_angle_d1.855397
X-RAY DIFFRACTIONf_dihedral_angle_d30.498120
X-RAY DIFFRACTIONf_chiral_restr0.15147
X-RAY DIFFRACTIONf_plane_restr0.00851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.806-1.91890.38361330.34991169X-RAY DIFFRACTION98
1.9189-2.06710.25961290.27381182X-RAY DIFFRACTION99
2.0671-2.27510.23311290.22281181X-RAY DIFFRACTION99
2.2751-2.60420.24621320.20991208X-RAY DIFFRACTION100
2.6042-3.28090.20011380.21121187X-RAY DIFFRACTION100
3.2809-42.1450.22131280.18231204X-RAY DIFFRACTION99

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