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- PDB-6g41: Crystal structure of SeMet-labeled mavirus penton protein -

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Basic information

Entry
Database: PDB / ID: 6g41
TitleCrystal structure of SeMet-labeled 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 / SAD / Resolution: 2.9 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 20, 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: Minor capsid protein
B: Minor capsid protein
C: Minor capsid protein
D: Minor capsid protein
E: Minor capsid protein
F: Minor capsid protein
G: Minor capsid protein
H: Minor capsid protein
I: Minor capsid protein
J: Minor capsid protein


Theoretical massNumber of molelcules
Total (without water)358,56010
Polymers358,56010
Non-polymers00
Water00
1
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)179,2805
Polymers179,2805
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Minor capsid protein
G: Minor capsid protein
H: Minor capsid protein
I: Minor capsid protein
J: Minor capsid protein


Theoretical massNumber of molelcules
Total (without water)179,2805
Polymers179,2805
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.790, 94.330, 156.380
Angle α, β, γ (deg.)90.000, 92.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
12A
22B
32C
42D
52E
13F
23H
33I
43J
14F
24G
34H
44I
54J
15F
25G
16F
26G
17A
27B
37C
47D
57E
18F
28G
38H
48I
58J

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPROPROAA3 - 2157 - 219
21GLNGLNPROPROBB3 - 2157 - 219
31GLNGLNPROPROCC3 - 2157 - 219
41GLNGLNPROPRODD3 - 2157 - 219
51GLNGLNPROPROEE3 - 2157 - 219
12ASPASPARGARGAA225 - 250229 - 254
22ASPASPARGARGBB225 - 250229 - 254
32ASPASPARGARGCC225 - 250229 - 254
42ASPASPARGARGDD225 - 250229 - 254
52ASPASPARGARGEE225 - 250229 - 254
13GLNGLNPROPROFF3 - 2157 - 219
23GLNGLNPROPROHH3 - 2157 - 219
33GLNGLNPROPROII3 - 2157 - 219
43GLNGLNPROPROJJ3 - 2157 - 219
14ASPASPARGARGFF225 - 250229 - 254
24ASPASPARGARGGG225 - 250229 - 254
34ASPASPARGARGHH225 - 250229 - 254
44ASPASPARGARGII225 - 250229 - 254
54ASPASPARGARGJJ225 - 250229 - 254
15GLNGLNSERSERFF3 - 137 - 17
25GLNGLNSERSERGG3 - 137 - 17
16PROPROPROPROFF27 - 21531 - 219
26PROPROPROPROGG27 - 21531 - 219
17TYRTYRSERSERAA258 - 301262 - 305
27TYRTYRSERSERBB258 - 301262 - 305
37TYRTYRSERSERCC258 - 301262 - 305
47TYRTYRSERSERDD258 - 301262 - 305
57TYRTYRSERSEREE258 - 301262 - 305
18TYRTYRSERSERFF258 - 301262 - 305
28TYRTYRSERSERGG258 - 301262 - 305
38TYRTYRSERSERHH258 - 301262 - 305
48TYRTYRSERSERII258 - 301262 - 305
58TYRTYRSERSERJJ258 - 301262 - 305

NCS ensembles :
ID
1
2
3
4
5
6
7
8

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.327349, -0.941111, -0.084569), (0.940585, 0.333092, -0.065946), (0.090232, -0.057957, 0.994233)62.222301, 11.88653, 0.6587
3given(-0.806549, -0.589525, -0.044037), (0.589288, -0.795818, -0.139333), (0.047095, -0.13833, 0.989266)70.533867, 70.950027, 5.61544
4given(-0.813403, 0.581142, 0.025502), (-0.577858, -0.802221, -0.150074), (-0.066756, -0.136807, 0.988346)18.71711, 101.082077, 8.09099
5given(0.3108, 0.948159, 0.066318), (-0.946421, 0.315157, -0.070448), (-0.087697, -0.040869, 0.995309)-27.56621, 57.749809, 4.19412
6given(1), (1), (1)
7given(0.313043, -0.946047, -0.083654), (0.946021, 0.318392, -0.060583), (0.083949, -0.060173, 0.994652)62.695621, 11.16856, 0.92102
8given(-0.816061, -0.576099, -0.046423), (0.576655, -0.806172, -0.132495), (0.038905, -0.134894, 0.990096)70.732933, 70.343277, 5.48408
9given(-0.803522, 0.594809, 0.023549), (-0.591956, -0.794244, -0.136988), (-0.062778, -0.124013, 0.990293)18.33736, 98.690231, 7.2496
10given(0.317118, 0.945934, 0.06816), (-0.94484, 0.321325, -0.063467), (-0.081937, -0.044274, 0.995654)-27.84165, 56.310181, 4.23269
11given(1), (1), (1)
12given(-0.810399, -0.583731, 0.050108), (0.585656, -0.809479, 0.041845), (0.016135, 0.063257, 0.997867)72.136238, 61.21756, -3.21274
13given(-0.808479, 0.587346, 0.037223), (-0.586012, -0.809254, 0.041212), (0.054329, 0.011506, 0.998457)20.77, 94.035683, -1.41724
14given(0.318684, 0.947799, -0.010873), (-0.946967, 0.318861, 0.039761), (0.041152, -0.002374, 0.99915)-22.83761, 53.414539, -0.87573
15given(1), (1), (1)
16given(0.299809, -0.953083, 0.041806), (0.953901, 0.30012, 0.00121), (-0.0137, 0.039516, 0.999125)58.413639, 4.66703, -1.37363
17given(-0.811232, -0.582461, 0.051403), (0.584277, -0.810912, 0.032287), (0.022877, 0.056226, 0.998156)72.046494, 62.11932, -2.92647
18given(-0.805529, 0.591878, 0.028338), (-0.589713, -0.805426, 0.059388), (0.057975, 0.031127, 0.997833)21.17259, 92.375679, -2.82103
19given(0.321597, 0.946873, -0.002591), (-0.946017, 0.321421, 0.041728), (0.040344, -0.010969, 0.999126)-23.567511, 53.008362, -0.47878
20given(1), (1), (1)
21given(0.322489, -0.945924, 0.035045), (0.946497, 0.321773, -0.0246), (0.011994, 0.041103, 0.999083)58.415249, 6.67576, -1.85969
22given(1), (1), (1)
23given(0.311589, -0.949093, 0.046198), (0.950112, 0.311909, -0.000282), (-0.014142, 0.043981, 0.998932)57.686661, 4.4485, -1.42399
24given(1), (1), (1)
25given(0.330947, -0.939918, -0.083835), (0.94021, 0.336015, -0.055667), (0.080492, -0.0604, 0.994924)62.089199, 10.23598, 0.93728
26given(-0.804128, -0.592978, -0.041894), (0.592413, -0.793533, -0.139111), (0.049246, -0.136682, 0.98939)70.254349, 70.90358, 5.51001
27given(-0.812955, 0.581517, 0.030697), (-0.579614, -0.80296, -0.138934), (-0.056144, -0.130739, 0.989826)17.90254, 99.271393, 7.5784
28given(0.300185, 0.951106, 0.072712), (-0.950039, 0.304941, -0.066613), (-0.085529, -0.049083, 0.995126)-28.41437, 57.842831, 4.63064
29given(1), (1), (1)
30given(0.298031, -0.95353, 0.044249), (0.954525, 0.298075, -0.005767), (-0.007691, 0.043955, 0.999004)58.257439, 5.28976, -1.55472
31given(-0.810552, -0.58307, 0.055095), (0.585107, -0.810298, 0.032665), (0.025597, 0.058713, 0.997947)71.643883, 62.044949, -3.05589
32given(-0.800868, 0.598148, 0.028803), (-0.596571, -0.801092, 0.048526), (0.052099, 0.02168, 0.998407)20.56568, 93.149712, -2.06638
33given(0.320926, 0.947023, -0.012432), (-0.946266, 0.321167, 0.037849), (0.039837, -0.000383, 0.999206)-22.75128, 53.395229, -0.94205

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Components

#1: Protein
Minor capsid protein


Mass: 35855.984 Da / Num. of mol.: 10
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
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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 0.37 M NaCl, 24% PEG3350

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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: 2.9→49.09 Å / Num. obs: 163213 / % possible obs: 99.3 % / Redundancy: 20.938 % / Biso Wilson estimate: 60 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.142 / Χ2: 1.148 / Net I/σ(I): 19.04 / Num. measured all: 3417378 / Scaling rejects: 7314
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-319.9910.6825.4931420115875157170.9570.799
3-3.220.3510.458.352632226130258620.9820.46199
3.2-3.321.9310.32311.8123488610797107100.9910.33199.2
3.3-3.422.0210.26213.68209327957895060.9930.26899.2
3.4-3.521.950.23415.64185742853084620.9940.2499.2
3.5-3.621.7610.19717.42162030748874460.9950.20299.4
3.6-3.821.4680.16719.7427627512931128690.9960.17199.5
3.8-420.1460.14521.6120868810405103590.9970.14899.6
4-521.2790.1226.664653430517303830.9980.12399.6
5-620.3080.10528.3127303513500134450.9980.10799.6
6-1020.8220.0931.6830216414547145120.9990.09299.8
10-49.0919.8310.06840.9378174399739420.9990.0798.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.09 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 19.064 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2695 4171 5 %RANDOM
Rwork0.2144 ---
obs0.2171 79241 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 163.85 Å2 / Biso mean: 69.559 Å2 / Biso min: 31.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å2-1.52 Å2
2--5.04 Å20 Å2
3----3.57 Å2
Refinement stepCycle: final / Resolution: 2.9→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24476 0 0 0 24476
Num. residues----2976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01925038
X-RAY DIFFRACTIONr_bond_other_d0.0060.0223032
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.95333979
X-RAY DIFFRACTIONr_angle_other_deg0.859353047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17452960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13625.2041370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.032154148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0851599
X-RAY DIFFRACTIONr_chiral_restr0.0710.23771
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0228572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026011
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3356MEDIUM POSITIONAL0.450.5
12B3356MEDIUM POSITIONAL0.370.5
13C3356MEDIUM POSITIONAL0.380.5
14D3356MEDIUM POSITIONAL0.390.5
15E3356MEDIUM POSITIONAL0.380.5
11A3356MEDIUM THERMAL18.032
12B3356MEDIUM THERMAL9.222
13C3356MEDIUM THERMAL10.262
14D3356MEDIUM THERMAL20.992
15E3356MEDIUM THERMAL9.632
21A426MEDIUM POSITIONAL0.520.5
22B426MEDIUM POSITIONAL0.250.5
23C426MEDIUM POSITIONAL0.270.5
24D426MEDIUM POSITIONAL0.380.5
25E426MEDIUM POSITIONAL0.310.5
21A426MEDIUM THERMAL14.542
22B426MEDIUM THERMAL8.682
23C426MEDIUM THERMAL7.432
24D426MEDIUM THERMAL11.692
25E426MEDIUM THERMAL10.222
31F3356MEDIUM POSITIONAL0.320.5
32H3356MEDIUM POSITIONAL0.330.5
33I3356MEDIUM POSITIONAL0.360.5
34J3356MEDIUM POSITIONAL0.330.5
31F3356MEDIUM THERMAL7.912
32H3356MEDIUM THERMAL7.082
33I3356MEDIUM THERMAL6.442
34J3356MEDIUM THERMAL6.172
41F426MEDIUM POSITIONAL0.220.5
42G426MEDIUM POSITIONAL0.280.5
43H426MEDIUM POSITIONAL0.360.5
44I426MEDIUM POSITIONAL0.320.5
45J426MEDIUM POSITIONAL0.410.5
41F426MEDIUM THERMAL6.052
42G426MEDIUM THERMAL6.12
43H426MEDIUM THERMAL4.852
44I426MEDIUM THERMAL5.282
45J426MEDIUM THERMAL6.172
51F192MEDIUM POSITIONAL0.350.5
51F192MEDIUM THERMAL10.292
61F2954MEDIUM POSITIONAL0.240.5
61F2954MEDIUM THERMAL8.832
71A744MEDIUM POSITIONAL0.390.5
72B744MEDIUM POSITIONAL0.340.5
73C744MEDIUM POSITIONAL0.420.5
74D744MEDIUM POSITIONAL0.450.5
75E744MEDIUM POSITIONAL0.340.5
71A744MEDIUM THERMAL17.232
72B744MEDIUM THERMAL7.932
73C744MEDIUM THERMAL9.882
74D744MEDIUM THERMAL12.742
75E744MEDIUM THERMAL6.132
81F744MEDIUM POSITIONAL0.350.5
82G744MEDIUM POSITIONAL0.390.5
83H744MEDIUM POSITIONAL0.270.5
84I744MEDIUM POSITIONAL0.360.5
85J744MEDIUM POSITIONAL0.350.5
81F744MEDIUM THERMAL4.682
82G744MEDIUM THERMAL10.652
83H744MEDIUM THERMAL4.922
84I744MEDIUM THERMAL4.942
85J744MEDIUM THERMAL7.622
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 305 -
Rwork0.333 5794 -
all-6099 -
obs--98.83 %

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