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- PDB-6yfj: Virus-like particle of bacteriophage ESE001 -

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Basic information

Entry
Database: PDB / ID: 6yfj
TitleVirus-like particle of bacteriophage ESE001
Componentscoat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Biological speciesLeviviridae sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.233 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)750,13460
Polymers750,13460
Non-polymers00
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

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

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


Theoretical massNumber of molelcules
Total (without water)2,250,402180
Polymers2,250,402180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area821000 Å2
ΔGint-5509 kcal/mol
Surface area917550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)283.345, 283.345, 666.042
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ...
coat protein


Mass: 12502.233 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leviviridae sp. (virus) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationY

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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: 6.86 Å3/Da / Density % sol: 82.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 30% MPD, 5 mM DTT, 0.1 M sodium acetate pH 4.6

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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: 3.23→48.944 Å / Num. obs: 312312 / % possible obs: 97.9 % / Redundancy: 3.597 % / Biso Wilson estimate: 76.166 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.284 / Rrim(I) all: 0.332 / Χ2: 1.182 / Net I/σ(I): 4.36 / Num. measured all: 1123399
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
3.23-3.433.4311.7380.5816522651471481560.2352.04393.6
3.43-3.663.7961.1790.9618207048390479590.4081.36799.1
3.66-3.953.6910.7431.5716425145017445000.6150.86598.9
3.95-4.333.5730.4312.7714613141394409030.8440.50498.8
4.33-4.843.6830.2245.8713714237556372340.9530.2699.1
4.84-5.573.5090.1996.2611402433107324970.960.23398.2
5.57-6.813.7680.1826.9610435227996276920.9710.21198.9
6.81-9.533.3530.08612.87186421776214300.9920.10198.4
9.53-48.9443.2110.05718.053833912450119410.9950.06795.9

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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: 3.233→48.944 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.2324 10007 3.22 %
Rwork0.2317 --
obs0.2317 310956 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 349.34 Å2 / Biso mean: 97.9671 Å2 / Biso min: 26.21 Å2
Refinement stepCycle: final / Resolution: 3.233→48.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52380 0 0 0 52380
Num. residues----7080
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.233-3.26970.37182220.3835694968
3.2697-3.30810.37143330.3747980995
3.3081-3.34840.39473450.37091008598
3.3484-3.39080.36123390.35571015399
3.3908-3.43540.36823500.34711019899
3.4354-3.48250.35253270.34551023999
3.4825-3.53220.33483500.33731013899
3.5322-3.58490.32633070.32841031999
3.5849-3.64090.32413530.32271012499
3.6409-3.70060.34053440.32761015999
3.7006-3.76440.29093400.30141024599
3.7644-3.83280.28393450.2951018999
3.8328-3.90650.27273200.28031005799
3.9065-3.98620.29123490.27761021198
3.9862-4.07280.2693340.26521002498
4.0728-4.16750.25133460.2511021199
4.1675-4.27170.22063550.21991014899
4.2717-4.38710.20383220.20071025099
4.3871-4.51610.18273680.18821021099
4.5161-4.66180.17933130.17651023999
4.6618-4.82830.17033430.17441016199
4.8283-5.02140.18643380.17811011999
5.0214-5.24970.19333450.18561009698
5.2497-5.52610.18913360.19071006698
5.5261-5.87180.20413280.20291016999
5.8718-6.32430.22843310.20941016799
6.3243-6.95910.19753400.19241016099
6.9591-7.96240.18793490.17461009098
7.9624-10.01760.15553210.15891015199
10.0176-48.9440.20063140.221981395

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