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- PDB-8jvn: Crystal structure of the mk2h_deltaMILPYS peptide homodimer, DZBB form -

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Basic information

Entry
Database: PDB / ID: 8jvn
TitleCrystal structure of the 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: 1.404 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)5,4124
Polymers5,1241
Non-polymers2883
Water57632
1
A: mk2h_deltaMILPYS
hetero molecules

A: mk2h_deltaMILPYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8258
Polymers10,2482
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4850 Å2
ΔGint-109 kcal/mol
Surface area5210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.077, 34.077, 54.288
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-229-

HOH

21A-231-

HOH

31A-232-

HOH

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Components

#1: Protein/peptide mk2h_deltaMILPYS


Mass: 5124.123 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.: 32 / 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: 1.78 Å3/Da / Density % sol: 30.73 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 13165 / % possible obs: 97 % / Redundancy: 2.3 % / CC1/2: 0.99 / Net I/σ(I): 0.14
Reflection shellResolution: 1.4→1.5 Å / Num. unique obs: 2111 / 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: 1.404→29.512 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 1315 10.08 %
Rwork0.1881 --
obs0.1901 13042 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.404→29.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms332 0 15 32 379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015343
X-RAY DIFFRACTIONf_angle_d1.195458
X-RAY DIFFRACTIONf_dihedral_angle_d21.972133
X-RAY DIFFRACTIONf_chiral_restr0.10954
X-RAY DIFFRACTIONf_plane_restr0.00556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4043-1.46050.36911360.29021222X-RAY DIFFRACTION87
1.4605-1.5270.29281510.25161346X-RAY DIFFRACTION98
1.527-1.60740.31141590.23191333X-RAY DIFFRACTION97
1.6074-1.70820.29071430.22661368X-RAY DIFFRACTION98
1.7082-1.840.231520.21951327X-RAY DIFFRACTION97
1.84-2.02510.25481490.22111299X-RAY DIFFRACTION95
2.0251-2.31810.20041430.20171325X-RAY DIFFRACTION97
2.3181-2.92010.21781420.191313X-RAY DIFFRACTION94
2.9201-29.5120.17141400.15681194X-RAY DIFFRACTION87

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