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- PDB-4rft: T=1 subviral particle of Grouper nervous necrosis virus capsid pr... -

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Basic information

Entry
Database: PDB / ID: 4rft
TitleT=1 subviral particle of Grouper nervous necrosis virus capsid protein deletion mutant (delta 1-34 & 218-338)
ComponentsCoat protein
KeywordsVIRUS / Shell domain
Function / homology
Function and homology information


viral capsid / metal ion binding
Similarity search - Function
Nodavirus capsid / nodavirus capsid protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Capsid protein alpha
Similarity search - Component
Biological speciesEpinephelus coioides nervous necrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChen, N.C. / Chen, C.J. / Yoshimura, M. / Guan, H.H. / Chen, T.Y.
CitationJournal: Plos Pathog. / Year: 2015
Title: Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection
Authors: Chen, N.C. / Yoshimura, M. / Guan, H.H. / Wang, T.Y. / Misumi, Y. / Lin, C.C. / Chuankhayan, P. / Nakagawa, A. / Chan, S.I. / Tsukihara, T. / Chen, T.Y. / Chen, C.J.
History
DepositionSep 27, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: Coat protein
Q: Coat protein
R: Coat protein
S: Coat protein
T: Coat protein
U: Coat protein
V: Coat protein
W: Coat protein
X: Coat protein
Y: Coat protein
Z: Coat protein
0: Coat protein
1: Coat protein
2: Coat protein
3: Coat protein
4: Coat protein
5: Coat protein
6: Coat protein
7: Coat protein
8: Coat protein
9: Coat protein
a: Coat protein
b: Coat protein
c: Coat protein
d: Coat protein
e: Coat protein
f: Coat protein
g: Coat protein
h: Coat protein
i: Coat protein
j: Coat protein
k: Coat protein
l: Coat protein
m: Coat protein
n: Coat protein
o: Coat protein
p: Coat protein
q: Coat protein
r: Coat protein
s: Coat protein
t: Coat protein
u: Coat protein
v: Coat protein
w: Coat protein
x: Coat protein


Theoretical massNumber of molelcules
Total (without water)1,189,03860
Polymers1,189,03860
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area194050 Å2
ΔGint-547 kcal/mol
Surface area291550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)288.947, 288.947, 175.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein ...
Coat protein


Mass: 19817.297 Da / Num. of mol.: 60 / Fragment: UNP residues 35-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epinephelus coioides nervous necrosis virus
Production host: Escherichia coli (E. coli) / References: UniProt: Q8JNX5
Sequence detailsAUTHOR STATED T214N WAS NATURAL MUTATION ISOLATED FROM NORMAL GROUPER FISH.

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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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M NaCl, 0.1M Lithium sulfate, 0.1M MES, pH 6.5, 30% (w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 8, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 255496 / Num. obs: 255496 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.21 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIZ

4wiz


Resolution: 3.1→26.37 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.829 / SU B: 27.566 / SU ML: 0.455 / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28825 12823 5 %RANDOM
Rwork0.23815 ---
all0.24064 255496 --
obs0.24064 242663 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 3.1→26.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms75180 0 0 0 75180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01976860
X-RAY DIFFRACTIONr_bond_other_d0.0020.0272820
X-RAY DIFFRACTIONr_angle_refined_deg1.591.951105180
X-RAY DIFFRACTIONr_angle_other_deg0.9283166600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.12759720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00722.9093300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.0761511760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.79515720
X-RAY DIFFRACTIONr_chiral_restr0.0870.212300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02187600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0217880
X-RAY DIFFRACTIONr_mcbond_it3.7435.32339060
X-RAY DIFFRACTIONr_mcbond_other3.7435.32339059
X-RAY DIFFRACTIONr_mcangle_it6.437.96248720
X-RAY DIFFRACTIONr_mcangle_other6.437.96348721
X-RAY DIFFRACTIONr_scbond_it3.8265.80737800
X-RAY DIFFRACTIONr_scbond_other3.8265.80737801
X-RAY DIFFRACTIONr_scangle_other6.4968.55256461
X-RAY DIFFRACTIONr_long_range_B_refined11.543.11783587
X-RAY DIFFRACTIONr_long_range_B_other11.543.11883588
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 938 -
Rwork0.35 17415 -
obs--95.45 %

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