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- PDB-6yfr: Virus-like particle of bacteriophage NT-391 -

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Basic information

Entry
Database: PDB / ID: 6yfr
TitleVirus-like particle of bacteriophage NT-391
Componentscoat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Biological speciesLeviviridae sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 20, 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)804,07360
Polymers804,07360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area248520 Å2
ΔGint-2236 kcal/mol
Surface area310590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.917, 162.066, 162.976
Angle α, β, γ (deg.)71.160, 66.670, 66.830
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
coat protein


Mass: 13401.212 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: 4.4 Å3/Da / Density % sol: 72.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 34% MPD, 0.1 M sodium nitrate, 0.1M 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: Jan 24, 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: 2.6→51.88 Å / Num. all: 294001 / Num. obs: 294001 / % possible obs: 69.7 % / Redundancy: 2.3 % / Rpim(I) all: 0.178 / Rrim(I) all: 0.3 / Rsym value: 0.239 / Net I/av σ(I): 2.5 / Net I/σ(I): 2.5 / Num. measured all: 690098
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.742.11.1340.571242346430.8751.441.1340.556.2
2.74-2.912.10.9550.667141326230.7391.2140.9550.655.9
2.91-3.112.20.7120.983483385500.5440.9010.7120.870.3
3.11-3.362.20.4941.379810362040.3780.6250.4941.371.1
3.36-3.682.30.3142.174658328330.2380.3960.3142.269.9
3.68-4.112.50.2322.886393344610.1720.290.2323.281.2
4.11-4.752.60.1723.673753280970.1260.2140.1724.775.1
4.75-5.812.80.155474107269400.1110.1920.1555.185.4
5.81-8.222.70.1414.250350188870.1010.1740.1415.277.5
8.22-51.882.70.1054.729161107630.0750.130.1057.280.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
FFTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ms2

2ms2


Resolution: 2.6→51.88 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 38.71
RfactorNum. reflection% reflection
Rfree0.3231 9703 3.39 %
Rwork0.3175 --
obs0.3177 286598 67.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.01 Å2 / Biso mean: 50.2534 Å2 / Biso min: 15.56 Å2
Refinement stepCycle: final / Resolution: 2.6→51.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56340 0 0 0 56340
Num. residues----7380
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.62940.38362360.4064690451
2.6294-2.66030.40472520.3989688951
2.6603-2.69270.40752290.3976695751
2.6927-2.72680.44052550.4078687651
2.7268-2.76270.42212460.3951687551
2.7627-2.80060.4052520.3894676450
2.8006-2.84060.37882340.3938627446
2.8406-2.8830.38172450.3989727653
2.883-2.9280.41053250.3874874365
2.928-2.9760.38473060.3739931569
2.976-3.02730.34753430.3703946569
3.0273-3.08240.37983540.3695965271
3.0824-3.14160.37163440.3552966071
3.1416-3.20570.34012850.3467973471
3.2057-3.27540.31733530.34971572
3.2754-3.35160.33033340.3392956770
3.3516-3.43540.35793250.3147930768
3.4354-3.52830.31992960.3291831961
3.5283-3.63210.30313500.31161028776
3.6321-3.74930.30973910.311091380
3.7493-3.88320.31643710.311113681
3.8832-4.03870.30823820.30931100681
4.0387-4.22240.29673800.31011083080
4.2224-4.44490.33653920.29991042477
4.4449-4.72320.29523270.2855910167
4.7232-5.08760.30474040.29411168585
5.0876-5.59910.30253890.29021136484
5.5991-6.4080.30043770.29751077679
6.408-8.06850.28893530.28871015675
8.0685-51.880.28443730.27821092580

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