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- PDB-8jvx: Crystal structure of the dimeric DZBB fold protein mkaL2_v1.2_Z -

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Basic information

Entry
Database: PDB / ID: 8jvx
TitleCrystal structure of the dimeric DZBB fold protein mkaL2_v1.2_Z
ComponentsmkaL2_v1.2_Z
KeywordsDNA BINDING PROTEIN / Double zeta beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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: mkaL2_v1.2_Z
B: mkaL2_v1.2_Z


Theoretical massNumber of molelcules
Total (without water)9,0192
Polymers9,0192
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-23 kcal/mol
Surface area5030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.463, 37.705, 52.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide mkaL2_v1.2_Z


Mass: 4509.491 Da / Num. of mol.: 2
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.: 43 / 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: 1.88 Å3/Da / Density % sol: 34.63 %
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-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 23, 2023
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: 12049 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.991 / Net I/σ(I): 10.51
Reflection shellResolution: 1.8→1.91 Å / Num. unique obs: 1919 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.801→30.573 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 1199 9.96 %
Rwork0.2032 --
obs0.2048 12041 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→30.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms583 0 0 43 626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014603
X-RAY DIFFRACTIONf_angle_d1.47808
X-RAY DIFFRACTIONf_dihedral_angle_d36.19245
X-RAY DIFFRACTIONf_chiral_restr0.705100
X-RAY DIFFRACTIONf_plane_restr0.008100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8012-1.87330.31981370.30131197X-RAY DIFFRACTION98
1.8733-1.95860.2811310.26171191X-RAY DIFFRACTION99
1.9586-2.06180.21081320.2341202X-RAY DIFFRACTION99
2.0618-2.19090.21211370.21051214X-RAY DIFFRACTION99
2.1909-2.360.28571300.2081208X-RAY DIFFRACTION99
2.36-2.59740.21181310.21891191X-RAY DIFFRACTION98
2.5974-2.9730.23431330.20331219X-RAY DIFFRACTION100
2.973-3.74460.20091320.18591221X-RAY DIFFRACTION100
3.7446-30.5730.19021360.18261199X-RAY DIFFRACTION99

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