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- PDB-6yfn: Virus-like particle of bacteriophage ESE058 -

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Basic information

Entry
Database: PDB / ID: 6yfn
TitleVirus-like particle of bacteriophage ESE058
Componentscoat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Biological speciesLeviviridae sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.189 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)1,455,547120
Polymers1,454,34490
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)2,911,093240
Polymers2,908,689180
Non-polymers2,40560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1114790 Å2
ΔGint-7744 kcal/mol
Surface area897870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)500.893, 500.893, 287.055
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ...
coat protein


Mass: 16159.382 Da / Num. of mol.: 90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leviviridae sp. (virus) / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12.5% PEG 1000, 7% PEG 8000

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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: Nov 4, 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: 3.189→49.258 Å / Num. obs: 680195 / % possible obs: 99.8 % / Redundancy: 10.224 % / Biso Wilson estimate: 53.059 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.796 / Rrim(I) all: 0.838 / Χ2: 1.184 / Net I/σ(I): 3.68
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
3.19-3.3810.2013.730.6111034761094911081770.2343.92598.8
3.38-3.6110.2442.0821.1410537941028881028670.4712.191100
3.61-3.99.7721.4611.693765095970959560.6191.543100
3.9-4.2710.7160.9892.5694653088352883310.811.038100
4.27-4.7710.4840.5764.4383986480126801090.9230.606100
4.77-5.510.1290.5074.871704470800707940.9280.534100
5.5-6.7110.6230.4725.2563822860079600790.9430.496100
6.71-9.419.9310.2299.4646560046887468840.9890.241100
9.41-49.2589.3410.10918.0725218527257269980.9970.11699

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Processing

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

2ms2


Resolution: 3.189→49.258 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.13
RfactorNum. reflection% reflection
Rfree0.2342 9955 1.47 %
Rwork0.2308 --
obs0.2309 677292 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 241.23 Å2 / Biso mean: 60.4553 Å2 / Biso min: 11.31 Å2
Refinement stepCycle: final / Resolution: 3.189→49.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms101460 0 30 0 101490
Biso mean--78.52 --
Num. residues----12990
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.189-3.2250.40232890.38661947188
3.225-3.2630.36233280.37532200899
3.263-3.30270.37983310.371222185100
3.3027-3.34450.38543320.362622204100
3.3445-3.38850.35913290.352622262100
3.3885-3.4350.3573320.333122285100
3.435-3.4840.30733370.318722267100
3.484-3.5360.3463280.316422247100
3.536-3.59120.29513340.307222297100
3.5912-3.65010.28743350.306922289100
3.6501-3.7130.30613320.322269100
3.713-3.78050.29693300.291922292100
3.7805-3.85320.27483340.283122337100
3.8532-3.93180.25093360.258622297100
3.9318-4.01730.24193310.246722249100
4.0173-4.11070.22823330.231822335100
4.1107-4.21340.23033290.225622346100
4.2134-4.32730.23383330.214122252100
4.3273-4.45450.21523300.194622352100
4.4545-4.59820.19343320.179922336100
4.5982-4.76240.15443350.165222380100
4.7624-4.95290.17973310.1722392100
4.9529-5.17810.16593370.17222345100
5.1781-5.45080.17533310.165522414100
5.4508-5.79180.17683360.173922366100
5.7918-6.23820.16933380.177922505100
6.2382-6.86450.16983340.16622473100
6.8645-7.85430.15243370.15322476100
7.8543-9.88250.15483380.155722631100
9.8825-49.2580.2283430.21862277599

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