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- PDB-6g45: Crystal structure of mavirus major capsid protein -

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Basic information

Entry
Database: PDB / ID: 6g45
TitleCrystal structure of mavirus major capsid protein
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: 2.5 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)200,3815
Polymers200,1963
Non-polymers1842
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.050, 137.050, 138.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 2 - 504 / Label seq-ID: 6 - 508

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.062585, -0.997994, -0.009504), (-0.054439, -0.012922, 0.998434), (-0.996554, -0.061969, -0.055138)-1.71644, 0.45706, -2.41527
3given(0.065881, -0.04855, -0.996646), (-0.997789, -0.011926, -0.065376), (-0.008712, 0.99875, -0.049228)-2.18904, -1.84874, -0.58042

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Components

#1: Protein Putative major capsid protein


Mass: 66732.125 Da / Num. of mol.: 3
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3 - 1.6 M ammonium sulfate, 19-25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.68 Å / Num. obs: 88504 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.09 % / Biso Wilson estimate: 50.013 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.137 / Χ2: 0.972 / Net I/σ(I): 13.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.610.3160.7723.7197040.8890.812100
2.6-2.710.2290.5724.9783280.9350.602100
2.7-2.89.7610.4715.8971780.9480.497100
2.8-2.99.7480.3767.2762450.9640.397100
2.9-310.3830.3058.9854310.9790.3299.9
3-3.210.5080.23611.5689670.9880.248100
3.2-3.310.4250.1814.4336860.9910.189100
3.3-3.410.3340.15216.3432740.9920.16100
3.4-3.510.180.14216.4729420.9920.15100
3.5-3.69.7050.13317.1826130.9940.14100
3.6-3.89.6590.13216.9644330.9920.139100
3.8-410.3180.10420.7636050.9950.109100
4-510.250.08125.14106250.9960.086100
5-69.4290.07924.247540.9950.083100
6-109.840.07426.7751970.9960.078100
10-48.689.0150.06729.5915220.9930.07198.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G44

6g44


Resolution: 2.5→48.68 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.009 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.222
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 4407 5 %RANDOM
Rwork0.2129 ---
obs0.2139 84097 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.13 Å2 / Biso mean: 44.291 Å2 / Biso min: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2---0.35 Å20 Å2
3---0.31 Å2
Refinement stepCycle: final / Resolution: 2.5→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11649 0 12 68 11729
Biso mean--65.48 33.63 -
Num. residues----1509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211911
X-RAY DIFFRACTIONr_bond_other_d0.020.0211004
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.96816189
X-RAY DIFFRACTIONr_angle_other_deg0.869325678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49851506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0125.349516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.184151989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7191545
X-RAY DIFFRACTIONr_chiral_restr0.0670.21841
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022241
Refine LS restraints NCS

Ens-ID: 1 / Number: 7547 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.20.5
2BMEDIUM POSITIONAL0.220.5
3CMEDIUM POSITIONAL0.190.5
1AMEDIUM THERMAL1.492
2BMEDIUM THERMAL1.522
3CMEDIUM THERMAL1.372
LS refinement shellResolution: 2.501→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 318 -
Rwork0.313 6129 -
all-6447 -
obs--99.72 %

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