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- PDB-8jvo: Crystal structure of the chemically synthesized mk2h_deltaMILPYS ... -

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Basic information

Entry
Database: PDB / ID: 8jvo
TitleCrystal structure of the chemically synthesized mk2h_deltaMILPYS peptide homodimer, DZBB form
Componentsmk2h_deltaMILPYS
KeywordsDNA BINDING PROTEIN / Double zeta beta barrel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 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: mk2h_deltaMILPYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9734
Polymers4,6851
Non-polymers2883
Water73941
1
A: mk2h_deltaMILPYS
hetero molecules

A: mk2h_deltaMILPYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9468
Polymers9,3692
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4880 Å2
ΔGint-108 kcal/mol
Surface area5170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.705, 33.705, 54.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

21A-241-

HOH

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Components

#1: Protein/peptide mk2h_deltaMILPYS


Mass: 4684.594 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% PEG 400, 100mM Tris pH8.5, 200mM Lithium sulfate

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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: 1.7→50 Å / Num. obs: 7683 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC1/2: 0.99 / Net I/σ(I): 0.21
Reflection shellResolution: 1.7→1.8 Å / Num. unique obs: 1215 / 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: 1.701→29.189 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 761 9.94 %
Rwork0.1969 --
obs0.1984 7657 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.701→29.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms328 0 15 41 384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016339
X-RAY DIFFRACTIONf_angle_d1.55453
X-RAY DIFFRACTIONf_dihedral_angle_d26.011132
X-RAY DIFFRACTIONf_chiral_restr0.12554
X-RAY DIFFRACTIONf_plane_restr0.00755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.8320.29741660.25341368X-RAY DIFFRACTION99
1.832-2.01640.2571420.22151398X-RAY DIFFRACTION100
2.0164-2.3080.22531370.20661373X-RAY DIFFRACTION100
2.308-2.90750.2331680.21821371X-RAY DIFFRACTION100
2.9075-29.1890.17711480.17111386X-RAY DIFFRACTION100

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