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- PDB-7c21: Crystal structure of Duvenhage virus phosphoprotein C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7c21
TitleCrystal structure of Duvenhage virus phosphoprotein C-terminal domain
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / phosphoprotein
Function / homology
Function and homology information


: / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase activity / cytoplasm
Similarity search - Function
Phosphoprotein / Phosphoprotein, C-terminal / : / Phosphoprotein
Similarity search - Domain/homology
Biological speciesDuvenhage virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSugiyama, A. / Jiang, X. / Maenaka, K. / Yao, M. / Ose, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K07296 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural comparison of the C-terminal domain of functionally divergent lyssavirus P proteins.
Authors: Sugiyama, A. / Nomai, T. / Jiang, X. / Minami, M. / Yao, M. / Maenaka, K. / Ito, N. / Gooley, P.R. / Moseley, G.W. / Ose, T.
History
DepositionMay 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)12,8711
Polymers12,8711
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.190, 49.520, 25.280
Angle α, β, γ (deg.)90.00, 99.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphoprotein / Protein P / Protein M1


Mass: 12870.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Duvenhage virus / Production host: Escherichia coli (E. coli) / References: UniProt: D2CRL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH7.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→43.8 Å / Num. obs: 8380 / % possible obs: 98 % / Redundancy: 8.6 % / Biso Wilson estimate: 23.57 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.216 / Net I/σ(I): 7.53
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 1361 / CC1/2: 0.607 / Rrim(I) all: 1.385 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYI

1vyi


Resolution: 1.95→43.8 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.09
RfactorNum. reflection% reflection
Rfree0.2645 585 6.99 %
Rwork0.198 --
obs0.2027 8366 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 0 52 892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007854
X-RAY DIFFRACTIONf_angle_d0.831143
X-RAY DIFFRACTIONf_dihedral_angle_d2.895532
X-RAY DIFFRACTIONf_chiral_restr0.043125
X-RAY DIFFRACTIONf_plane_restr0.005146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.14620.30071460.2151914X-RAY DIFFRACTION97
2.1462-2.45680.27471340.20661941X-RAY DIFFRACTION98
2.4568-3.09520.27891430.20451970X-RAY DIFFRACTION99
3.0952-43.80.2471620.18761956X-RAY DIFFRACTION98

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