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- PDB-6yff: Virus-like particle of Beihai levi-like virus 21 -

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Basic information

Entry
Database: PDB / ID: 6yff
TitleVirus-like particle of Beihai levi-like virus 21
Componentscoat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Biological speciesBeihai levi-like virus 21
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.089 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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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


Theoretical massNumber of molelcules
Total (without water)622,11845
Polymers622,11845
Non-polymers00
Water0
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

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

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

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


Theoretical massNumber of molelcules
Total (without water)2,488,472180
Polymers2,488,472180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)296.937, 306.875, 322.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ...
coat protein


Mass: 13824.843 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beihai levi-like virus 21 / 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: 5.91 Å3/Da / Density % sol: 79.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 400, 0.2 M sodium citrate, 0.1 M Tris-HCl pH 8.5

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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: Jan 27, 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: 3.089→48.938 Å / Num. obs: 264708 / % possible obs: 99.1 % / Redundancy: 5.665 % / Biso Wilson estimate: 66.517 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.358 / Rrim(I) all: 0.395 / Χ2: 1.087 / Net I/σ(I): 5.56
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
3.09-3.285.5422.7850.5822630542787408340.2213.07495.4
3.28-3.55.7031.5021.1322935940256402190.4761.65599.9
3.5-3.785.8790.8172.1922035537518374820.9750.89799.9
3.78-4.145.4810.5673.1218898834548344810.8380.62799.8
4.14-4.625.9060.286.4518508931357313410.9620.30799.9
4.62-5.335.6850.2038.3815743327725276910.9770.22499.9
5.33-6.515.7470.1898.8813549423593235750.9770.20899.9
6.51-9.125.5010.10214.3610119918452183950.9950.11399.7
9.12-48.9385.170.04628.485526210828106900.9980.05198.7

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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
Resolution: 3.089→48.938 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.79
RfactorNum. reflection% reflection
Rfree0.271 9929 3.77 %
Rwork0.2661 --
obs0.2663 263402 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 312.9 Å2 / Biso mean: 80.8487 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 3.089→48.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43650 0 0 0 43650
Num. residues----5670
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0894-3.12450.38072340.392593470
3.1245-3.16120.37153140.3808833698
3.1612-3.19980.3843530.3832841199
3.1998-3.24030.37673070.3789845499
3.2403-3.28290.35913440.37448480100
3.2829-3.32780.39583480.37778438100
3.3278-3.37540.37293210.37098521100
3.3754-3.42570.35853470.35288506100
3.4257-3.47930.3713110.34798534100
3.4793-3.53630.33273610.32868479100
3.5363-3.59720.3323400.31498454100
3.5972-3.66260.3193050.3148571100
3.6626-3.73310.30233280.30668493100
3.7331-3.80920.31483350.31438550100
3.8092-3.8920.33123400.30858500100
3.892-3.98250.30683520.29718509100
3.9825-4.08210.29243200.28398491100
4.0821-4.19240.29143420.28128532100
4.1924-4.31570.27643400.25638555100
4.3157-4.45490.25133230.24448545100
4.4549-4.6140.22973450.23068536100
4.614-4.79860.22423260.21628528100
4.7986-5.01680.23533380.22478553100
5.0168-5.2810.25993510.2358569100
5.281-5.61140.23123290.22888572100
5.6114-6.04390.20853360.21928602100
6.0439-6.65080.21283200.22928644100
6.6508-7.61010.23393490.22368638100
7.6101-9.57610.18033360.18168709100
9.5761-48.9380.22753340.2264882999

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