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- PDB-6g43: Crystal structure of SeMet-labeled mavirus major capsid protein l... -

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Basic information

Entry
Database: PDB / ID: 6g43
TitleCrystal structure of SeMet-labeled 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 / SAD / Resolution: 2.4 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 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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


Theoretical massNumber of molelcules
Total (without water)173,4093
Polymers173,4093
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.350, 135.300, 136.040
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: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 2 - 516 / Label seq-ID: 6 - 520

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.002781, -0.001373, 0.999995), (-0.999996, 6.4E-5, 0.002782), (-6.8E-5, -0.999999, -0.001373)-0.94578, 135.008102, 136.083755
3given(0.002446, -0.999997, -0.000356), (-0.002627, 0.00035, -0.999996), (0.999994, 0.002447, -0.002626)135.090836, 136.233185, 0.86951

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Components

#1: Protein Putative major capsid protein


Mass: 57802.895 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.75 %
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: 2.4→48 Å / Num. obs: 188659 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.816 % / Biso Wilson estimate: 37.223 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.122 / Χ2: 1.42 / Net I/σ(I): 20.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.513.3230.6095.51217230.9310.633100
2.5-2.613.620.4927.18185080.9590.511100
2.6-2.713.5270.3839.03159620.9750.398100
2.7-2.814.3570.31211.31136250.9830.323100
2.8-314.3390.22914.41222610.9910.238100
3-3.213.6310.16318.2170070.9950.169100
3.2-3.814.0320.10225.92320350.9980.106100
3.8-413.8160.07831.1468480.9980.081100
4-613.6660.06137.74286350.9990.063100
6-813.8760.05640.1869900.9990.059100
8-1013.9960.04549.1524860.9990.047100
10-1212.8370.04151.6910950.9990.042100
12-1513.6390.03954.267360.9990.041100
15-2015.4620.03956.8943910.04100
20-4814.2690.04156.583090.9990.04393.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SHELXDphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.775 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.206
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 4902 5 %RANDOM
Rwork0.2134 ---
obs0.2145 93137 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.45 Å2 / Biso mean: 31.291 Å2 / Biso min: 13.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2---0.26 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 2.4→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11925 0 0 175 12100
Biso mean---22.7 -
Num. residues----1545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912177
X-RAY DIFFRACTIONr_bond_other_d0.0210.0211640
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.98116545
X-RAY DIFFRACTIONr_angle_other_deg0.889326850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53451542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16825.367531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.694151914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3611548
X-RAY DIFFRACTIONr_chiral_restr0.0660.21875
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02113935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022679
Refine LS restraints NCS

Ens-ID: 1 / Number: 7855 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.210.5
2BMEDIUM POSITIONAL0.220.5
3CMEDIUM POSITIONAL0.180.5
1AMEDIUM THERMAL0.652
2BMEDIUM THERMAL0.552
3CMEDIUM THERMAL0.582
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 359 -
Rwork0.306 6825 -
all-7184 -
obs--99.97 %

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