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- PDB-6g42: Crystal structure of mavirus penton protein -

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Basic information

Entry
Database: PDB / ID: 6g42
TitleCrystal structure of mavirus penton protein
ComponentsMinor capsid protein
KeywordsVIRAL PROTEIN / single jelly-roll / capsid protein / virus
Function / homologyMinor capsid protein
Function and homology information
Biological speciesCafeteriavirus-dependent mavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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Assembly

Deposited unit
A: Minor capsid protein
B: Minor capsid protein
C: Minor capsid protein
D: Minor capsid protein
E: Minor capsid protein


Theoretical massNumber of molelcules
Total (without water)177,8735
Polymers177,8735
Non-polymers00
Water1448
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)95.240, 131.100, 154.210
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
41D
51E

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSERAA3 - 2167 - 220
21GLNGLNSERSERBB3 - 2167 - 220
31GLNGLNSERSERCC3 - 2167 - 220
41GLNGLNSERSERDD3 - 2167 - 220
51GLNGLNSERSEREE3 - 2167 - 220
12THRTHRPHEPHEAA222 - 249226 - 253
22THRTHRPHEPHEBB222 - 249226 - 253
32THRTHRPHEPHECC222 - 249226 - 253
42THRTHRPHEPHEDD222 - 249226 - 253
52THRTHRPHEPHEEE222 - 249226 - 253
13HISHISILEILEAA259 - 302263 - 306
23HISHISILEILEBB259 - 302263 - 306
33HISHISILEILECC259 - 302263 - 306
43HISHISILEILEDD259 - 302263 - 306
53HISHISILEILEEE259 - 302263 - 306

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.292614, 0.954804, 0.052212), (-0.955566, 0.29401, -0.021259), (-0.035649, -0.043671, 0.99841)-15.79209, -24.11598, -1.05115
3given(-0.82308, 0.565941, 0.047437), (-0.567915, -0.820703, -0.062607), (0.003499, -0.078471, 0.99691)-42.961361, -16.259781, -0.08099
4given(-0.794558, -0.606913, 0.018305), (0.603663, -0.792829, -0.083748), (0.06534, -0.055493, 0.996319)-43.522221, 11.6268, 1.10254
5given(0.315198, -0.949006, -0.00615), (0.947326, 0.315014, -0.05778), (0.056771, 0.012386, 0.99831)-17.37348, 21.467569, 0.80438

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Components

#1: Protein
Minor capsid protein


Mass: 35574.613 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cafeteriavirus-dependent mavirus / Gene: MV17, Mvrk_gpp17 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: A0A1L4BKA3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 0.3 M NaCl, 26% PEG3350

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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: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→47.86 Å / Num. obs: 53606 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.68 % / Biso Wilson estimate: 61.524 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.093 / Χ2: 1.004 / Net I/σ(I): 16.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.86.6720.7213.0854460.8830.78399.6
2.8-2.96.5520.5094.3847260.9380.55399.6
2.9-36.7780.3845.9341210.9710.41699.7
3-3.26.9610.2778.1668020.9810.399.7
3.2-3.36.8010.19910.5728270.9890.21699.8
3.3-3.46.6460.15612.3124940.9910.1799.8
3.4-3.56.3760.12514.2422330.9940.13799.9
3.5-3.66.560.11215.8619730.9940.12299.9
3.6-3.86.8430.09119.0633790.9960.09999.9
3.8-46.90.07721.8327400.9970.08399.9
4-56.6110.05626.8881030.9970.06199.9
5-66.7920.05130.6636210.9970.05599.9
6-106.4090.04532.3639730.9980.049100
10-47.865.8710.03740.1111680.9960.04198.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G41

6g41


Resolution: 2.7→47.86 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 16.559 / SU ML: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 2681 5 %RANDOM
Rwork0.2203 ---
obs0.2229 50925 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.75 Å2 / Biso mean: 66.472 Å2 / Biso min: 34.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0 Å2-0 Å2
2---5.43 Å20 Å2
3---4.57 Å2
Refinement stepCycle: final / Resolution: 2.7→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12381 0 0 8 12389
Biso mean---44.17 -
Num. residues----1507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01912726
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211693
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.94617280
X-RAY DIFFRACTIONr_angle_other_deg0.861326942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36251512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67925.18695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.311152171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1581550
X-RAY DIFFRACTIONr_chiral_restr0.0720.21912
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023067
Refine LS restraints NCS

Ens-ID: 1 / Number: 4571 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.430.5
2BMEDIUM POSITIONAL0.380.5
3CMEDIUM POSITIONAL0.40.5
4DMEDIUM POSITIONAL0.440.5
5EMEDIUM POSITIONAL0.440.5
1AMEDIUM THERMAL6.212
2BMEDIUM THERMAL4.112
3CMEDIUM THERMAL5.422
4DMEDIUM THERMAL5.932
5EMEDIUM THERMAL6.312
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 194 -
Rwork0.391 3672 -
all-3866 -
obs--99.59 %

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