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- PDB-6dku: Crystal structure of Myotis VP35 mutant of interferon inhibitory ... -

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Basic information

Entry
Database: PDB / ID: 6dku
TitleCrystal structure of Myotis VP35 mutant of interferon inhibitory domain
ComponentsVP35
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polymerase cofactor VP35
Similarity search - Component
Biological speciesMyotis lucifugus (little brown bat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLiu, H. / Ginell, G.M. / Keefe, L.J. / Leung, D.W. / Amarasinghe, G.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109945 United States
CitationJournal: Cell Rep / Year: 2018
Title: Conservation of Structure and Immune Antagonist Functions of Filoviral VP35 Homologs Present in Microbat Genomes.
Authors: Edwards, M.R. / Liu, H. / Shabman, R.S. / Ginell, G.M. / Luthra, P. / Ramanan, P. / Keefe, L.J. / Kollner, B. / Amarasinghe, G.K. / Taylor, D.J. / Leung, D.W. / Basler, C.F.
History
DepositionMay 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / 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
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP35


Theoretical massNumber of molelcules
Total (without water)14,5061
Polymers14,5061
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, macromolecular assembly in solution was analyzed by SEC-MALS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.126, 78.126, 43.471
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein VP35


Mass: 14505.612 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myotis lucifugus (little brown bat) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9JKD1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.7711 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7711 Å / Relative weight: 1
ReflectionResolution: 2.6→39.063 Å / Num. obs: 4730 / % possible obs: 95.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 61.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0873 / Net I/σ(I): 11.97
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 1.42 / Num. unique obs: 409 / CC1/2: 0.609

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
autoPROC1.1.7data scaling
XDSOct 15,2015data reduction
XDSOct 15,2015data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L25

3l25


Resolution: 2.6→39.063 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.85
RfactorNum. reflection% reflection
Rfree0.2227 200 4.29 %
Rwork0.1711 --
obs0.1733 4662 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.03 Å2 / Biso mean: 67.7564 Å2 / Biso min: 33.61 Å2
Refinement stepCycle: final / Resolution: 2.6→39.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 0 7 998
Biso mean---56.36 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051015
X-RAY DIFFRACTIONf_angle_d0.7151379
X-RAY DIFFRACTIONf_chiral_restr0.049154
X-RAY DIFFRACTIONf_plane_restr0.005179
X-RAY DIFFRACTIONf_dihedral_angle_d10.857611
LS refinement shellResolution: 2.6001→39.0674 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2227 200 -
Rwork0.1711 4462 -
all-4662 -
obs--95 %
Refinement TLS params.Method: refined / Origin x: 4.1838 Å / Origin y: -30.9361 Å / Origin z: -5.2976 Å
111213212223313233
T0.3379 Å2-0.0023 Å2-0.0027 Å2-0.2759 Å20.0035 Å2--0.5509 Å2
L5.1033 °20.7509 °21.8696 °2-2.4753 °20.9395 °2--7.9976 °2
S0.1849 Å °-0.2503 Å °0.1916 Å °0.1078 Å °-0.0454 Å °0.2462 Å °-0.0886 Å °-0.251 Å °-0.0937 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA157 - 281
2X-RAY DIFFRACTION1allW1 - 7

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