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- PDB-6yfi: Bacteriophage EMS014 coat protein -

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Basic information

Entry
Database: PDB / ID: 6yfi
TitleBacteriophage EMS014 coat protein
Componentscoat protein
KeywordsVIRAL PROTEIN / virus / structural protein
Biological speciesLeviviridae sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.248 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 1.2May 1, 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

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Assembly

Deposited unit
A: coat protein
B: coat protein
C: coat protein
D: coat protein


Theoretical massNumber of molelcules
Total (without water)66,2044
Polymers66,2044
Non-polymers00
Water19,3841076
1
A: coat protein
B: coat protein


Theoretical massNumber of molelcules
Total (without water)33,1022
Polymers33,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-68 kcal/mol
Surface area12640 Å2
MethodPISA
2
C: coat protein
D: coat protein


Theoretical massNumber of molelcules
Total (without water)33,1022
Polymers33,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-69 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.558, 92.699, 94.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
coat protein


Mass: 16550.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leviviridae sp. (virus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1076 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 10% PEG 8000, 0.1 M sodium chloride, 0.05 M phosphate/citrate pH 4.2

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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: 1.248→48.615 Å / Num. obs: 173301 / % possible obs: 99.1 % / Redundancy: 6.405 % / Biso Wilson estimate: 21.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.092 / Χ2: 1.146 / Net I/σ(I): 8.51
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
1.25-1.326.0371.0541.0316014528026265270.8251.15294.7
1.32-1.416.7310.711.6617742426366263590.920.77100
1.41-1.536.4660.4272.7315887224614245710.9650.46499.8
1.53-1.676.6470.2365.1615063022677226610.9880.25699.9
1.67-1.876.6640.1518.5613683220548205320.9940.16499.9
1.87-2.166.3360.09614.5911541918230182150.9960.10499.9
2.16-2.646.2310.07919.69633615473154610.9960.08699.9
2.64-3.736.0390.06924.147282112078120590.9970.07599.8
3.73-48.6155.9960.05826.6241468693769160.9980.06399.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly(Ala) model of ESE021 CP dimer

Resolution: 1.248→42.21 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.1974 8618 4.99 %
Rwork0.1753 --
obs0.1764 172802 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.42 Å2 / Biso mean: 24.3684 Å2 / Biso min: 11.09 Å2
Refinement stepCycle: final / Resolution: 1.248→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4450 0 0 1076 5526
Biso mean---33.61 -
Num. residues----592
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2481-1.26220.42752010.4086396772
1.2622-1.27710.34762720.36215492100
1.2771-1.29270.38073030.3488541399
1.2927-1.3090.34922690.3381548899
1.309-1.32630.35632930.3187546299
1.3263-1.34440.31912830.29145478100
1.3444-1.36360.31542770.27745481100
1.3636-1.3840.25782910.255475100
1.384-1.40560.26623000.2385464100
1.4056-1.42870.27022730.2271550699
1.4287-1.45330.2552930.21365442100
1.4533-1.47970.24272940.20995484100
1.4797-1.50820.21913040.19125490100
1.5082-1.5390.24012910.1849545599
1.539-1.57240.2012790.1575483100
1.5724-1.6090.19172940.15245511100
1.609-1.64930.20682820.1545506100
1.6493-1.69380.19322850.155532100
1.6938-1.74370.17213000.1425503100
1.7437-1.80.18382840.15435515100
1.8-1.86430.18022860.15645514100
1.8643-1.93890.19542900.1635534100
1.9389-2.02720.1873040.15695519100
2.0272-2.13410.18392820.15835574100
2.1341-2.26780.1792980.15475563100
2.2678-2.44280.19132910.16565582100
2.4428-2.68860.19612940.17395586100
2.6886-3.07760.1972960.17295627100
3.0776-3.8770.17532940.165670100
3.877-42.210.16543150.16065868100

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