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- PDB-5g51: High resolution structure of the part of VP3 protein of Deformed ... -

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Basic information

Entry
Database: PDB / ID: 5g51
TitleHigh resolution structure of the part of VP3 protein of Deformed Wing Virus forming P-domain
ComponentsDWV-VP3-P-DOMAIN
KeywordsVIRAL PROTEIN / PICORNAVIRALES / PICORNAVIRALES IFLAVIRIDAE IFLAVIRUS DWV CAPSID P-DOMAIN JELLYROLL INHIBITOR ANTIVIRAL CATALYTIC SITE PROTEASE LIPASE ESTERASE RECEPTOR
Function / homologyRNA-directed RNA polymerase, catalytic domain / CRPV capsid protein like / RNA dependent RNA polymerase / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Dicistrovirus, capsid-polyprotein, C-terminal / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan ...RNA-directed RNA polymerase, catalytic domain / CRPV capsid protein like / RNA dependent RNA polymerase / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Dicistrovirus, capsid-polyprotein, C-terminal / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA helicase / cysteine-type peptidase activity / host cell membrane / RNA helicase activity / viral capsid / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
Specimen sourceDEFORMED WING VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.45 Å resolution
AuthorsSkubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of deformed wing virus, a major honey bee pathogen.
Authors: Karel Škubník / Jiří Nováček / Tibor Füzik / Antonín Přidal / Robert J Paxton / Pavel Plevka
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 18, 2016 / Release: Mar 22, 2017
RevisionDateData content typeGroupProviderType
1.0Mar 22, 2017Structure modelrepositoryInitial release
1.1Mar 29, 2017Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DWV-VP3-P-DOMAIN


Theoretical massNumber of molelcules
Total (without water)17,5361
Polyers17,5361
Non-polymers00
Water4,360242
1
A: DWV-VP3-P-DOMAIN

A: DWV-VP3-P-DOMAIN

A: DWV-VP3-P-DOMAIN

A: DWV-VP3-P-DOMAIN


Theoretical massNumber of molelcules
Total (without water)70,1424
Polyers70,1424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation2_555-x,-y,z1
Buried area (Å2)5700
ΔGint (kcal/M)-33.3
Surface area (Å2)27920
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)63.976, 104.922, 57.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC 2 2 2

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Components

#1: Protein/peptide DWV-VP3-P-DOMAIN


Mass: 17535.582 Da / Num. of mol.: 1 / Details: PART OF THE VP3 CHAIN OF THE DEFORMED WING VIRUS. / Fragment: P-DOMAIN, RESIDUES 260-398 / Source: (gene. exp.) DEFORMED WING VIRUS / Plasmid name: PET22T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8B3M2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Formula: H2O / Water
Sequence detailsSEQUENCE WILL BE UPLOAD SOON TO THE UNIPROT DATABASE.

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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: 3.16 / Density percent sol: 61.09 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 4.3 M NACL,

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SOLEIL BEAMLINE PROXIMA 1 / Synchrotron site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL
Detector: PIXEL / Collection date: Mar 24, 2016
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionD resolution high: 1.45 Å / D resolution low: 39.75 Å / Number obs: 34920 / Observed criterion sigma I: 2.1 / Rmerge I obs: 0.06 / NetI over sigmaI: 14.2 / Redundancy: 6.09 % / Percent possible obs: 99.9
Reflection shellRmerge I obs: 0.54 / Highest resolution: 1.45 Å / Lowest resolution: 1.47 Å / MeanI over sigI obs: 2.1 / Redundancy: 5.36 % / Percent possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.17 / Sigma F: 1.39 / Overall phase error: 22.09 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.212 / R factor R work: 0.1887 / R factor obs: 0.1899 / Highest resolution: 1.45 Å / Lowest resolution: 39.749 Å / Number reflection R free: 1754 / Number reflection obs: 34919 / Percent reflection R free: 5 / Percent reflection obs: 99.85
Refine hist #LASTHighest resolution: 1.45 Å / Lowest resolution: 39.749 Å
Number of atoms included #LASTProtein: 1242 / Nucleic acid: 0 / Ligand: 0 / Solvent: 242 / Total: 1484
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061520
X-RAY DIFFRACTIONf_angle_d1.0472099
X-RAY DIFFRACTIONf_dihedral_angle_d13.247575
X-RAY DIFFRACTIONf_chiral_restr0.045205
X-RAY DIFFRACTIONf_plane_restr0.005291
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.45000.35610.25901.4893115252499.00
1.48930.28840.24731.53311502507100.00
1.53310.28450.23381.58261352501100.00
1.58260.24560.24011.63911262539100.00
1.63910.25650.22191.70481272537100.00
1.70480.25160.20991.78231382506100.00
1.78230.21230.20201.87631382571100.00
1.87630.22770.19901.99391432511100.00
1.99390.20540.19662.14781472537100.00
2.14780.20260.19522.36391452552100.00
2.36390.25640.20252.70591202570100.00
2.70590.21190.18383.40891322604100.00
3.40890.16840.156639.76391382706100.00

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