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- PDB-6yfd: Virus-like particle of Beihai levi-like virus 14 -

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Basic information

Entry
Database: PDB / ID: 6yfd
TitleVirus-like particle of Beihai levi-like virus 14
Componentscoat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Biological speciesBeihai levi-like virus 14
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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)1,986,81990
Polymers1,986,81990
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)3,973,638180
Polymers3,973,638180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1611310 Å2
ΔGint-11229 kcal/mol
Surface area940950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)328.670, 373.710, 310.500
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: 22075.766 Da / Num. of mol.: 90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beihai levi-like virus 14 / 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: 4.8 Å3/Da / Density % sol: 74.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5% PEG 4000, 0.1 M magnesium chloride, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: Room-temperature data collection / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 22, 2019
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: 3.3→49.332 Å / Num. obs: 536242 / % possible obs: 94.4 % / Redundancy: 5.308 % / Biso Wilson estimate: 81.126 Å2 / CC1/2: 0.937 / Rmerge(I) obs: 0.647 / Rrim(I) all: 0.715 / Χ2: 0.823 / Net I/σ(I): 2.28 / Num. measured all: 2846288 / Scaling rejects: 376
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
3.3-3.52.4532.2550.4617193591282700840.1712.74776.8
3.5-3.734.6362.4590.7134363482260741230.2342.74390.1
3.73-4.035.9461.9181.0648028081054807670.3192.10999.6
4.03-4.415.9591.2141.6743685673637733120.5151.33699.6
4.41-4.936.0960.7542.6341023267580672930.7260.82999.6
4.93-5.685.7850.7032.7733862359023585320.7270.77899.2
5.68-6.936.1450.5683.530823950338501650.8180.62499.7
6.93-9.75.760.2755.7422549839476391520.9570.30399.2
9.7-49.3325.7420.1768.2413099123289228140.9830.19298

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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: 3.3→49.332 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.73
RfactorNum. reflection% reflection
Rfree0.267 9824 1.87 %
Rwork0.2649 --
obs0.2649 525683 92.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 263.36 Å2 / Biso mean: 92.1527 Å2 / Biso min: 26.5 Å2
Refinement stepCycle: final / Resolution: 3.3→49.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms126960 0 0 0 126960
Num. residues----17190
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.33750.391830.39561028256
3.3375-3.37680.38322340.38721154763
3.3768-3.41790.40162660.37871294970
3.4179-3.46120.36652300.37571359673
3.4612-3.50670.36662800.37921382675
3.5067-3.55470.40592780.3741400076
3.5547-3.60550.38912600.36791465079
3.6055-3.65930.37343510.36331829099
3.6593-3.71650.36933650.3631829099
3.7165-3.77740.34513460.3571837599
3.7774-3.84250.36663370.347918373100
3.8425-3.91230.36213680.345618406100
3.9123-3.98760.35983190.340918435100
3.9876-4.06890.3563530.32761825199
4.0689-4.15730.31573650.31951837399
4.1573-4.2540.29973550.305818509100
4.254-4.36030.29493400.294618392100
4.3603-4.47810.28363680.279518468100
4.4781-4.60980.25543330.264118492100
4.6098-4.75850.24843440.254118478100
4.7585-4.92840.23883710.2451845699
4.9284-5.12550.26113570.242318476100
5.1255-5.35860.2393330.24191836499
5.3586-5.64070.21323620.23411846499
5.6407-5.99350.22843570.227818566100
5.9935-6.45540.21073490.215218609100
6.4554-7.10330.1983490.197818654100
7.1033-8.12720.18433560.17571852399
8.1272-10.22440.17543510.17121881299
10.2244-49.3320.21343640.21271895398

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