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- PDB-6yfh: Virus-like particle of bacteriophage EMS014 -

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Basic information

Entry
Database: PDB / ID: 6yfh
TitleVirus-like particle of bacteriophage EMS014
Componentscoat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Biological speciesLeviviridae sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.893 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


Theoretical massNumber of molelcules
Total (without water)1,489,58090
Polymers1,489,58090
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
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

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


Theoretical massNumber of molelcules
Total (without water)2,979,160180
Polymers2,979,160180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1074740 Å2
ΔGint-8110 kcal/mol
Surface area901540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)287.110, 492.500, 553.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ...
coat protein


Mass: 16550.891 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)

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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: 6.57 Å3/Da / Density % sol: 81.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.55 M sodium malonate, 0.25% Jeffamine ED-2003, 0.05 M HEPES pH 7.0

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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: May 9, 2018
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: 3.89→49.41 Å / Num. obs: 351942 / % possible obs: 99.1 % / Redundancy: 4.609 % / Biso Wilson estimate: 76.728 Å2 / CC1/2: 0.836 / Rmerge(I) obs: 0.859 / Rrim(I) all: 0.968 / Χ2: 0.769 / Net I/σ(I): 2.26 / Num. measured all: 1622019
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
3.89-4.134.2963.1440.4723576856765548830.1363.57896.7
4.13-4.414.8112.0630.7925648853394533080.2772.31199.8
4.41-4.764.7581.1891.3623656449838497210.5181.33499.8
4.76-5.214.6481.2031.3121249545892457200.4831.35499.6
5.21-5.824.5211.0351.4918742641669414590.5281.16999.5
5.82-6.74.7920.8441.9417654836880368410.6720.94699.9
6.7-8.174.4150.4383.4613745431361311330.8860.49699.3
8.17-11.44.7560.1987.4811670424582245360.9750.22299.8
11.4-49.414.3630.112.346257214710143410.9950.11397.5

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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: 3.893→49.357 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.38
RfactorNum. reflection% reflection
Rfree0.2699 9855 2.85 %
Rwork0.2665 --
obs0.2666 346121 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 361.14 Å2 / Biso mean: 111.969 Å2 / Biso min: 14.45 Å2
Refinement stepCycle: final / Resolution: 3.893→49.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms104400 0 0 0 104400
Num. residues----14040
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.893-3.93680.36172490.3828848074
3.9368-3.98310.39392990.3821987787
3.9831-4.03160.3543060.37171020889
4.0316-4.08260.40283060.38141042892
4.0826-4.13630.3953130.37731100796
4.1363-4.1930.36093240.35951132199
4.193-4.25280.35213400.36181133699
4.2528-4.31630.36783280.34711385100
4.3163-4.38370.34713360.338411404100
4.3837-4.45550.3253430.323711362100
4.4555-4.53230.31653300.317911367100
4.5323-4.61470.2963370.302811453100
4.6147-4.70330.30483300.292111385100
4.7033-4.79930.3113260.29611423100
4.7993-4.90350.32313360.303111472100
4.9035-5.01750.30713350.306511456100
5.0175-5.14280.30453330.30651133799
5.1428-5.28170.29573400.30451137199
5.2817-5.4370.30423280.29841129199
5.437-5.61220.29243370.282411504100
5.6122-5.81250.27733310.284811469100
5.8125-6.04480.3063390.278711482100
6.0448-6.31940.25673360.257211483100
6.3194-6.65190.24093370.245311515100
6.6519-7.06750.23153320.227911489100
7.0675-7.61140.20633320.19381144799
7.6114-8.3740.15683440.15081147599
8.374-9.5780.11963390.119911613100
9.578-12.03830.12793380.13611640100
12.0383-49.3570.2043510.20411178699

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