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- PDB-4rfu: Crystal structure of truncated P-domain from Grouper nervous necr... -

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Basic information

Entry
Database: PDB / ID: 4rfu
TitleCrystal structure of truncated P-domain from Grouper nervous necrosis virus capsid protein at 1.2A
ComponentsCoat protein
KeywordsVIRAL PROTEIN / Protrusion domain
Function / homologyNodavirus capsid / nodavirus capsid protein / Viral coat protein subunit / viral capsid / metal ion binding / DI(HYDROXYETHYL)ETHER / Capsid protein alpha
Function and homology information
Biological speciesEpinephelus coioides nervous necrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,05110
Polymers41,4973
Non-polymers5557
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-34 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.982, 83.458, 85.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coat protein


Mass: 13832.235 Da / Num. of mol.: 3 / Fragment: UNP residues 215-338
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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ca acetate, 0.1M MES, pH 6.5, 10% (w/v) PEG 8000, 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: 1.2→30 Å / Num. all: 144895 / Num. obs: 144895 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.2→1.21 Å / % possible all: 91

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIZ

4wiz


Resolution: 1.2→20.762 Å / SU ML: 0.1 / σ(F): 1.33 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 7230 5 %RANDOM
Rwork0.175 ---
all0.1753 144895 --
obs0.1753 144647 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→20.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 33 542 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082853
X-RAY DIFFRACTIONf_angle_d1.0443895
X-RAY DIFFRACTIONf_dihedral_angle_d12.089993
X-RAY DIFFRACTIONf_chiral_restr0.069417
X-RAY DIFFRACTIONf_plane_restr0.005498
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21360.24442100.2512417691
1.2136-1.22790.2612160.2493438095
1.2279-1.24290.24212140.2376452399
1.2429-1.25860.25222740.2258449699
1.2586-1.27520.23172390.21944573100
1.2752-1.29260.20922110.20724553100
1.2926-1.31110.22282490.20574563100
1.3111-1.33070.20552360.20074590100
1.3307-1.35150.2242730.19764495100
1.3515-1.37360.21342340.18614606100
1.3736-1.39730.19942360.18444561100
1.3973-1.42270.19792270.18664593100
1.4227-1.45010.19452300.17634613100
1.4501-1.47960.17482250.17314579100
1.4796-1.51180.18032430.1684631100
1.5118-1.5470.18022210.17084572100
1.547-1.58560.19852380.16924572100
1.5856-1.62850.16382450.16334584100
1.6285-1.67640.18762410.17114612100
1.6764-1.73050.17762500.17054584100
1.7305-1.79230.19122220.16984619100
1.7923-1.8640.18852370.16864628100
1.864-1.94880.17812400.17264602100
1.9488-2.05140.18052760.16624584100
2.0514-2.17990.17292810.16554604100
2.1799-2.34790.18162490.1694636100
2.3479-2.58380.17872350.17974670100
2.5838-2.95680.18422400.1874718100
2.9568-3.72180.16052460.16514704100
3.7218-20.76550.15712920.158479698

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