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- PDB-4qyk: Crystal structure of a canine parvovirus variant -

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Basic information

Entry
Database: PDB / ID: 4qyk
TitleCrystal structure of a canine parvovirus variant
ComponentsCapsid protein VP1
KeywordsVIRUS / capsid protein
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesFeline panleukopenia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLukk, T. / Organtini, L.J. / Hafenstein, S.U.
CitationJournal: J.Virol. / Year: 2015
Title: Global Displacement of Canine Parvovirus by a Host-Adapted Variant: Structural Comparison between Pandemic Viruses with Distinct Host Ranges.
Authors: Organtini, L.J. / Allison, A.B. / Lukk, T. / Parrish, C.R. / Hafenstein, S.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Advisory
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Jan 28, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
E: Capsid protein VP1
J: Capsid protein VP1
N: Capsid protein VP1
Q: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
U: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
a: Capsid protein VP1
b: Capsid protein VP1
c: Capsid protein VP1
d: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,943,09660
Polymers1,942,36730
Non-polymers72930
Water0
1
A: Capsid protein VP1
E: Capsid protein VP1
J: Capsid protein VP1
N: Capsid protein VP1
Q: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
U: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
a: Capsid protein VP1
b: Capsid protein VP1
c: Capsid protein VP1
d: Capsid protein VP1
hetero molecules

A: Capsid protein VP1
E: Capsid protein VP1
J: Capsid protein VP1
N: Capsid protein VP1
Q: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
U: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
a: Capsid protein VP1
b: Capsid protein VP1
c: Capsid protein VP1
d: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,886,192120
Polymers3,884,73460
Non-polymers1,45860
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area1029320 Å2
ΔGint-5112 kcal/mol
Surface area817740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)453.100, 453.100, 319.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein ...
Capsid protein VP1 /


Mass: 64745.559 Da / Num. of mol.: 30 / Fragment: UNP residues 154-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline panleukopenia virus / Cell line: NLFK / Plasmid: pGEM5Z / Production host: Felis catus (domestic cat) / References: UniProt: P90456
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Mg

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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: 4.21 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 20% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.5→49.99 Å / Num. all: 411123 / Num. obs: 410828 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 43.96 Å2 / Rmerge(I) obs: 0.219 / Net I/σ(I): 8 / Scaling rejects: 920
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
3.5-3.566.70.4434.413466120205100
19.17-49.995.50.1445.914186258494

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Processing

Software
NameVersionClassificationNB
Aimless0.3.5data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→49.989 Å / SU ML: 0.29 / σ(F): 1.33 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 20516 5 %RANDOM
Rwork0.1803 ---
all0.237 411123 --
obs0.1824 410041 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.9 Å2 / Biso mean: 23.971 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms130560 0 30 0 130590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013134519
X-RAY DIFFRACTIONf_angle_d1.54184080
X-RAY DIFFRACTIONf_chiral_restr0.06719770
X-RAY DIFFRACTIONf_plane_restr0.00924330
X-RAY DIFFRACTIONf_dihedral_angle_d14.26348150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.53980.30037160.24031290313619100
3.5398-3.58140.27166990.21651287513574100
3.5814-3.62510.28466360.2241295713593100
3.6251-3.67090.26276850.21211289013575100
3.6709-3.71920.25686840.20551287113555100
3.7192-3.77020.24496770.19891290913586100
3.7702-3.8240.24747000.19461288113581100
3.824-3.88110.24056840.19411292813612100
3.8811-3.94170.23296850.19871290813593100
3.9417-4.00630.22516590.18491293513594100
4.0063-4.07530.22726980.19041292913627100
4.0753-4.14940.22336850.17811290913594100
4.1494-4.22920.21697120.17441294313655100
4.2292-4.31540.20476490.16941295413603100
4.3154-4.40920.21897130.17181291513628100
4.4092-4.51170.2136770.16631296513642100
4.5117-4.62450.20316840.16421297513659100
4.6245-4.74940.20117290.16591290513634100
4.7494-4.88910.20496630.16671298113644100
4.8891-5.04670.2046990.16921298413683100
5.0467-5.22690.19876660.16051306213728100
5.2269-5.4360.20666810.16721298813669100
5.436-5.6830.20716610.18191304713708100
5.683-5.98220.20796530.17861308013733100
5.9822-6.35630.19516970.1651306813765100
6.3563-6.84590.19726720.16351309913771100
6.8459-7.53280.2127000.16981311713817100
7.5328-8.6180.18167090.14821314013849100
8.618-10.83950.17856700.14971327913949100
10.8395-49.99440.24866730.2151131281380196

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