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- PDB-6yfe: Virus-like particle of Beihai levi-like virus 19 -

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Basic information

Entry
Database: PDB / ID: 6yfe
TitleVirus-like particle of Beihai levi-like virus 19
Componentscoat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Biological speciesBeihai levi-like virus 19
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.794 Å
AuthorsRumnieks, J. / Kalnins, G. / Sisovs, M. / Lieknina, I. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.1/16/A/104 Latvia
CitationJournal: Sci Adv / Year: 2020
Title: Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes.
Authors: Rumnieks, J. / Lieknina, I. / Kalnins, G. / Sisovs, M. / Akopjana, I. / Bogans, J. / Tars, K.
History
DepositionMar 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
AA: coat protein
AB: coat protein
AC: coat protein
AD: coat protein
AE: coat protein
AF: coat protein
AG: coat protein
AH: coat protein
AI: coat protein
AJ: coat protein
AK: coat protein
AL: coat protein
AM: coat protein
AN: coat protein
AO: coat protein
AP: coat protein
AQ: coat protein
AR: coat protein
AS: coat protein
AT: coat protein
AU: coat protein
AV: coat protein
AW: coat protein
AX: coat protein
AY: coat protein
AZ: coat protein
BA: coat protein
BB: coat protein
BC: coat protein
BD: coat protein
BE: coat protein
BF: coat protein
BG: coat protein
BH: coat protein
BI: coat protein
BJ: coat protein
BK: coat protein
BL: coat protein
BM: coat protein
BN: coat protein
BO: coat protein
BP: coat protein
BQ: coat protein
BR: coat protein
BS: coat protein
BT: coat protein
BU: coat protein
BV: coat protein
BW: coat protein
BX: coat protein
BY: coat protein
BZ: coat protein
CA: coat protein
CB: coat protein
CC: coat protein
CD: coat protein
CE: coat protein
CF: coat protein
CG: coat protein
CH: coat protein
CI: coat protein
CJ: coat protein
CK: coat protein
CL: coat protein
CM: coat protein
CN: coat protein
CO: coat protein
CP: coat protein
CQ: coat protein
CR: coat protein
CS: coat protein
CT: coat protein
CU: coat protein
CV: coat protein
CW: coat protein
CX: coat protein
CY: coat protein
CZ: coat protein
DA: coat protein
DB: coat protein
DC: coat protein
DD: coat protein
DE: coat protein
DF: coat protein
DG: coat protein
DH: coat protein
DI: coat protein
DJ: coat protein
DK: coat protein
DL: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,293,706120
Polymers1,292,50390
Non-polymers1,20230
Water00
1
AA: coat protein
AB: coat protein
AC: coat protein
AD: coat protein
AE: coat protein
AF: coat protein
AG: coat protein
AH: coat protein
AI: coat protein
AJ: coat protein
AK: coat protein
AL: coat protein
AM: coat protein
AN: coat protein
AO: coat protein
AP: coat protein
AQ: coat protein
AR: coat protein
AS: coat protein
AT: coat protein
AU: coat protein
AV: coat protein
AW: coat protein
AX: coat protein
AY: coat protein
AZ: coat protein
BA: coat protein
BB: coat protein
BC: coat protein
BD: coat protein
BE: coat protein
BF: coat protein
BG: coat protein
BH: coat protein
BI: coat protein
BJ: coat protein
BK: coat protein
BL: coat protein
BM: coat protein
BN: coat protein
BO: coat protein
BP: coat protein
BQ: coat protein
BR: coat protein
BS: coat protein
BT: coat protein
BU: coat protein
BV: coat protein
BW: coat protein
BX: coat protein
BY: coat protein
BZ: coat protein
CA: coat protein
CB: coat protein
CC: coat protein
CD: coat protein
CE: coat protein
CF: coat protein
CG: coat protein
CH: coat protein
CI: coat protein
CJ: coat protein
CK: coat protein
CL: coat protein
CM: coat protein
CN: coat protein
CO: coat protein
CP: coat protein
CQ: coat protein
CR: coat protein
CS: coat protein
CT: coat protein
CU: coat protein
CV: coat protein
CW: coat protein
CX: coat protein
CY: coat protein
CZ: coat protein
DA: coat protein
DB: coat protein
DC: coat protein
DD: coat protein
DE: coat protein
DF: coat protein
DG: coat protein
DH: coat protein
DI: coat protein
DJ: coat protein
DK: coat protein
DL: coat protein
hetero molecules

AA: coat protein
AB: coat protein
AC: coat protein
AD: coat protein
AE: coat protein
AF: coat protein
AG: coat protein
AH: coat protein
AI: coat protein
AJ: coat protein
AK: coat protein
AL: coat protein
AM: coat protein
AN: coat protein
AO: coat protein
AP: coat protein
AQ: coat protein
AR: coat protein
AS: coat protein
AT: coat protein
AU: coat protein
AV: coat protein
AW: coat protein
AX: coat protein
AY: coat protein
AZ: coat protein
BA: coat protein
BB: coat protein
BC: coat protein
BD: coat protein
BE: coat protein
BF: coat protein
BG: coat protein
BH: coat protein
BI: coat protein
BJ: coat protein
BK: coat protein
BL: coat protein
BM: coat protein
BN: coat protein
BO: coat protein
BP: coat protein
BQ: coat protein
BR: coat protein
BS: coat protein
BT: coat protein
BU: coat protein
BV: coat protein
BW: coat protein
BX: coat protein
BY: coat protein
BZ: coat protein
CA: coat protein
CB: coat protein
CC: coat protein
CD: coat protein
CE: coat protein
CF: coat protein
CG: coat protein
CH: coat protein
CI: coat protein
CJ: coat protein
CK: coat protein
CL: coat protein
CM: coat protein
CN: coat protein
CO: coat protein
CP: coat protein
CQ: coat protein
CR: coat protein
CS: coat protein
CT: coat protein
CU: coat protein
CV: coat protein
CW: coat protein
CX: coat protein
CY: coat protein
CZ: coat protein
DA: coat protein
DB: coat protein
DC: coat protein
DD: coat protein
DE: coat protein
DF: coat protein
DG: coat protein
DH: coat protein
DI: coat protein
DJ: coat protein
DK: coat protein
DL: coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,587,411240
Polymers2,585,007180
Non-polymers2,40560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area947040 Å2
ΔGint-7274 kcal/mol
Surface area862420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)298.111, 325.048, 346.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ...
coat protein


Mass: 14361.148 Da / Num. of mol.: 90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beihai levi-like virus 19 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: 6.49 Å3/Da / Density % sol: 81.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 66% MPD, 100 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 1, 2017
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.79→49.431 Å / Num. obs: 323225 / % possible obs: 98 % / Redundancy: 3.41 % / Biso Wilson estimate: 83.511 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.372 / Rrim(I) all: 0.44 / Χ2: 1.15 / Net I/σ(I): 3.55 / Num. measured all: 1102291
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.79-4.023.3581.4950.7716857852699502070.2431.77295.3
4.02-4.33.3871.0891.0716511649516487530.3881.29198.5
4.3-4.643.5570.5972.1316382246296460510.6810.70499.5
4.64-5.083.5210.4652.7214800642631420410.7670.54998.6
5.08-5.673.3290.4092.9312656138676380160.8020.48698.3
5.67-6.533.570.3443.5712170934254340930.8570.40599.5
6.53-7.973.3590.2245.229600329166285850.9410.26598
7.97-11.123.3180.09411.567482522901225510.990.11298.5
11.12-49.4312.9140.05815.63767113745129280.9950.0794.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
FFTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ms2

2ms2


Resolution: 3.794→41.392 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.06
RfactorNum. reflection% reflection
Rfree0.2668 9968 3.09 %
Rwork0.2609 --
obs0.2611 322856 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 324.19 Å2 / Biso mean: 107.1578 Å2 / Biso min: 13.04 Å2
Refinement stepCycle: final / Resolution: 3.794→41.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms89040 0 30 0 89070
Biso mean--64.79 --
Num. residues----11730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.7944-3.83750.40932700.3735856581
3.8375-3.88260.36663290.36971034699
3.8826-3.92990.37233380.36921044499
3.9299-3.97960.3713500.36151043299
3.9796-4.0320.36843350.35541041399
4.032-4.08720.3473110.35381019996
4.0872-4.14550.36523220.3471028797
4.1455-4.20730.29333350.333310570100
4.2073-4.2730.31263520.325710564100
4.273-4.3430.32083260.315710509100
4.343-4.41780.33163330.305710539100
4.4178-4.4980.27993440.29191051499
4.498-4.58440.28563230.28231055199
4.5844-4.67790.27633440.27351049899
4.6779-4.77940.24883110.27161047999
4.7794-4.89050.2763450.27281046598
4.8905-5.01260.29283290.27181046798
5.0126-5.14780.30433550.27831048199
5.1478-5.2990.26833190.26471047999
5.299-5.46970.27963180.25851022396
5.4697-5.66470.2473440.24710614100
5.6647-5.89090.24523560.241510584100
5.8909-6.15820.2223180.228410650100
6.1582-6.48170.23943520.22371057499
6.4817-6.88610.23183230.21861059199
6.8861-7.4150.2153370.20451053098
7.415-8.1560.17643370.17491030696
8.156-9.32450.16023360.15431075399
9.3245-11.70370.15043440.15491072099
11.7037-41.3920.29633320.27131054194

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