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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 / homology
Function and homology information


cysteine-type peptidase activity / host cell membrane / viral capsid / viral RNA genome replication / RNA helicase activity / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / structural molecule activity / RNA binding / membrane / ATP binding
Helicase, superfamily 3, single-stranded DNA/RNA virus / P-loop containing nucleoside triphosphate hydrolase / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Dicistrovirus, capsid-polyprotein, C-terminal / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Genome polyprotein
Biological speciesDEFORMED WING VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSkubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database 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
Polymers17,5361
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
Polymers70,1424
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 area5700 Å2
ΔGint-33.3 kcal/mol
Surface area27920 Å2
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-MC222
Components on special symmetry positions
IDModelComponents
11A-2113-

HOH

21A-2161-

HOH

31A-2209-

HOH

41A-2230-

HOH

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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 method: isolated from a genetically manipulated source
Source: (gene. exp.) DEFORMED WING VIRUS / Plasmid: PET22T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8B3M2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % 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 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2016
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→39.75 Å / Num. obs: 34920 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 6.09 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.36 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→39.749 Å / SU ML: 0.17 / σ(F): 1.39 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1754 5 %
Rwork0.1887 --
Obs0.1899 34919 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→39.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 0 242 1484
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0061520
f_angle_d1.0472099
f_dihedral_angle_d13.247575
f_chiral_restr0.045205
f_plane_restr0.005291
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.45-1.48930.35611150.259252499
1.4893-1.53310.28841500.24732507100
1.5331-1.58260.28451350.23382501100
1.5826-1.63910.24561260.24012539100
1.6391-1.70480.25651270.22192537100
1.7048-1.78230.25161380.20992506100
1.7823-1.87630.21231380.2022571100
1.8763-1.99390.22771430.1992511100
1.9939-2.14780.20541470.19662537100
2.1478-2.36390.20261450.19522552100
2.3639-2.70590.25641200.20252570100
2.7059-3.40890.21191320.18382604100
3.4089-39.76390.16841380.15662706100

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