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- PDB-6g44: Crystal structure of mavirus major capsid protein lacking the C-t... -

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Basic information

Entry
Database: PDB / ID: 6g44
TitleCrystal structure of mavirus major capsid protein lacking the C-terminal domain
ComponentsPutative major capsid protein
KeywordsVIRAL PROTEIN / double jelly-roll / capsid protein / virus
Function / homology: / Major capsid protein V20 C-terminal domain / Putative major capsid protein
Function and homology information
Biological speciesCafeteriavirus-dependent mavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBorn, D. / Reuter, L. / Meinhart, A. / Reinstein, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Capsid protein structure, self-assembly, and processing reveal morphogenesis of the marine virophage mavirus.
Authors: Born, D. / Reuter, L. / Mersdorf, U. / Mueller, M. / Fischer, M.G. / Meinhart, A. / Reinstein, J.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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: Putative major capsid protein
B: Putative major capsid protein
C: Putative major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,94734
Polymers171,0173
Non-polymers2,93031
Water30,4991693
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31850 Å2
ΔGint-508 kcal/mol
Surface area52220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.190, 132.580, 135.220
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 Putative major capsid protein


Mass: 57005.684 Da / Num. of mol.: 3 / Mutation: wildtype residues 517-606 were deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cafeteriavirus-dependent mavirus / Gene: MV18, Mvrk_gpp18 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RIL / References: UniProt: A0A1L4BK98
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1693 / 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: 3.44 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1 M tri-sodium citrate, 1.2 - 1.7 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→47.33 Å / Num. obs: 372727 / % possible obs: 99.6 % / Redundancy: 5.575 % / Biso Wilson estimate: 23.515 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.085 / Χ2: 0.988 / Net I/σ(I): 12.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.65.550.413.95651830.8910.45299.7
1.6-1.75.3920.265.9505310.950.28899.2
1.7-1.85.5780.1758.56402330.9750.19399.9
1.8-25.7620.11612.33582520.9880.12899.7
2-2.55.6260.07917.4766960.9930.08799.6
2.5-35.5790.06820.67340970.9940.07599.6
3-45.5360.06223.23272880.9950.06999.7
4-65.3330.0624.34142210.9950.06699.8
6-85.5950.05826.2835290.9950.06499.6
8-105.8160.0627.2812890.9930.06699.6
10-125.6870.05727.275790.9950.06399.8
12-155.4990.05726.583970.9950.06399.7
15-205.3490.05726.392490.9950.064100
20-47.334.4810.06423.91830.9760.07390.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G43

6g43


Resolution: 1.5→47.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.962 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1829 18637 5 %RANDOM
Rwork0.1649 ---
obs0.1658 354090 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.7 Å2 / Biso mean: 17.596 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.5→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11840 0 167 1693 13700
Biso mean--25.97 28.59 -
Num. residues----1535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212735
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211807
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.98117414
X-RAY DIFFRACTIONr_angle_other_deg0.918327665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16351695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50825.382550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.807152186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.4811552
X-RAY DIFFRACTIONr_chiral_restr0.090.22000
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114208
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022384
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 1372 -
Rwork0.237 26056 -
all-27428 -
obs--99.77 %

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