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- PDB-6yfa: Virus-like particle of bacteriophage AVE015 -

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Basic information

Entry
Database: PDB / ID: 6yfa
TitleVirus-like particle of bacteriophage AVE015
Componentscoat protein
KeywordsVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
Biological speciesLeviviridae sp. (virus)
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 ...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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,121,64780
Polymers1,120,84560
Non-polymers80220
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
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
hetero molecules

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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,364,940240
Polymers3,362,536180
Non-polymers2,40560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Unit cell
Length a, b, c (Å)559.310, 559.310, 559.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein ...
coat protein


Mass: 18680.754 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)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: 6.5 Å3/Da / Density % sol: 81.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 22% MPD, 0.1 M sodium nitrate, 0.1 M 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: 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: 3.3→61.766 Å / Num. all: 430490 / Num. obs: 430490 / % possible obs: 100 % / Redundancy: 18.9 % / Rpim(I) all: 0.165 / Rrim(I) all: 0.721 / Rsym value: 0.702 / Net I/av σ(I): 1.1 / Net I/σ(I): 4.6 / Num. measured all: 8135712
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
3.3-3.4818.62.890.31163480626560.6872.9712.891.1100
3.48-3.6919.52.0310.41156838593460.4712.0852.0311.6100
3.69-3.9418.81.4490.51049127557440.3421.4891.4492.2100
3.94-4.2617.70.9720.8917483518980.2371.0010.9723.1100
4.26-4.6719.60.6051.3938550478550.140.6220.6055.3100
4.67-5.2219.50.4961.5843400432770.1150.5090.4966.2100
5.22-6.0218.60.441.7713018382660.1050.4530.446.2100
6.02-7.3819.80.3322.3640930323880.0760.3410.3327.7100
7.38-10.4418.20.1923.5457483251190.0460.1980.19212.1100
10.44-61.76618.30.1194.4255403139410.0290.1230.11916.299.5

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Processing

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

2ms2


Resolution: 3.3→61.765 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.81
RfactorNum. reflection% reflection
Rfree0.2331 9978 2.32 %
Rwork0.2312 --
obs0.2313 429748 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.71 Å2 / Biso mean: 66.5179 Å2 / Biso min: 28.91 Å2
Refinement stepCycle: final / Resolution: 3.3→61.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms78960 0 20 0 78980
Biso mean--59.46 --
Num. residues----10020
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.33750.35463320.356213950100
3.3375-3.37680.34683300.346213930100
3.3768-3.41790.30843320.329713921100
3.4179-3.46120.33393340.323114087100
3.4612-3.50670.28063310.318513832100
3.5067-3.55480.30643350.311513985100
3.5548-3.60560.30663350.308413972100
3.6056-3.65940.34513330.306813981100
3.6594-3.71650.28253260.286713908100
3.7165-3.77750.2613350.275414015100
3.7775-3.84260.27853340.27313941100
3.8426-3.91250.28273350.279613992100
3.9125-3.98770.30693310.282713910100
3.9877-4.06910.27243340.267414016100
4.0691-4.15750.28873300.262313907100
4.1575-4.25420.23793350.236214055100
4.2542-4.36060.23113320.228413923100
4.3606-4.47850.20813270.210813921100
4.4785-4.61020.20383320.198413934100
4.6102-4.75890.18733320.198713959100
4.7589-4.9290.18963370.192913942100
4.929-5.12620.22153300.191514007100
5.1262-5.35940.18893270.188913935100
5.3594-5.64180.19093290.187814038100
5.6418-5.9950.18273320.186214058100
5.995-6.45740.18413320.182914009100
6.4574-7.10640.17283350.171314062100
7.1064-8.13270.16943360.164614117100
8.1327-10.23880.14743360.148414122100
10.2388-61.7650.22673390.22511434199

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