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- PDB-6x0r: A Circular Permutant of the Tobacco Mosaic Virus (TMV) mutant Q101H -

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Basic information

Entry
Database: PDB / ID: 6x0r
TitleA Circular Permutant of the Tobacco Mosaic Virus (TMV) mutant Q101H
ComponentsCapsid protein Circular Permutant
KeywordsVIRAL PROTEIN / Viral capsid proteins / self-assembling proteins / double-disk assembly
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein
Function and homology information
Biological speciesTobacco mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDai, J. / Knott, G.J. / Francis, M.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DEAC02-05CH1123 United States
CitationJournal: Acs Nano / Year: 2021
Title: Protein-Embedded Metalloporphyrin Arrays Templated by Circularly Permuted Tobacco Mosaic Virus Coat Proteins.
Authors: Dai, J. / Knott, G.J. / Fu, W. / Lin, T.W. / Furst, A.L. / Britt, R.D. / Francis, M.B.
History
DepositionMay 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: 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: Capsid protein Circular Permutant
B: Capsid protein Circular Permutant
C: Capsid protein Circular Permutant
D: Capsid protein Circular Permutant
E: Capsid protein Circular Permutant
F: Capsid protein Circular Permutant
G: Capsid protein Circular Permutant
H: Capsid protein Circular Permutant
I: Capsid protein Circular Permutant
J: Capsid protein Circular Permutant
K: Capsid protein Circular Permutant
L: Capsid protein Circular Permutant
M: Capsid protein Circular Permutant
N: Capsid protein Circular Permutant
O: Capsid protein Circular Permutant
P: Capsid protein Circular Permutant
Q: Capsid protein Circular Permutant


Theoretical massNumber of molelcules
Total (without water)301,14817
Polymers301,14817
Non-polymers00
Water00
1
A: Capsid protein Circular Permutant
B: Capsid protein Circular Permutant
C: Capsid protein Circular Permutant
D: Capsid protein Circular Permutant
E: Capsid protein Circular Permutant
F: Capsid protein Circular Permutant
G: Capsid protein Circular Permutant
H: Capsid protein Circular Permutant
I: Capsid protein Circular Permutant
J: Capsid protein Circular Permutant
K: Capsid protein Circular Permutant
L: Capsid protein Circular Permutant
M: Capsid protein Circular Permutant
N: Capsid protein Circular Permutant
O: Capsid protein Circular Permutant
P: Capsid protein Circular Permutant
Q: Capsid protein Circular Permutant

A: Capsid protein Circular Permutant
B: Capsid protein Circular Permutant
C: Capsid protein Circular Permutant
D: Capsid protein Circular Permutant
E: Capsid protein Circular Permutant
F: Capsid protein Circular Permutant
G: Capsid protein Circular Permutant
H: Capsid protein Circular Permutant
I: Capsid protein Circular Permutant
J: Capsid protein Circular Permutant
K: Capsid protein Circular Permutant
L: Capsid protein Circular Permutant
M: Capsid protein Circular Permutant
N: Capsid protein Circular Permutant
O: Capsid protein Circular Permutant
P: Capsid protein Circular Permutant
Q: Capsid protein Circular Permutant


Theoretical massNumber of molelcules
Total (without water)602,29734
Polymers602,29734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area86340 Å2
ΔGint-303 kcal/mol
Surface area190670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.697, 176.213, 102.248
Angle α, β, γ (deg.)90.000, 99.155, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 13 - 152 / Label seq-ID: 13 - 152

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB
33chain 'C'CC
44chain 'D'DD
55chain 'E'EE
66chain 'F'FF
77chain 'G'GG
88chain 'H'HH
99chain 'I'II
1010chain 'J'JJ
1111chain 'K'KK
1212chain 'L'LL
1313chain 'M'MM
1414chain 'N'NN
1515chain 'O'OO
1616chain 'P'PP
1717chain 'Q'QQ

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Components

#1: Protein
Capsid protein Circular Permutant / Coat protein


Mass: 17714.609 Da / Num. of mol.: 17 / Mutation: Q101H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco mosaic virus (strain vulgare) / Strain: vulgare / Gene: CP / Production host: Escherichia coli (E. coli) / References: UniProt: P69687

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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: 3.23 Å3/Da / Density % sol: 61.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M SPG buffer (0.0125 M succinic acid, 0.0438 M sodium phosphate, 0.0437 M glycine), 12%-18% (v/v) PEG 1500, pH 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.81→136.52 Å / Num. obs: 91158 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 69.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.8
Reflection shellResolution: 2.81→2.86 Å / Redundancy: 6 % / Num. unique obs: 4016 / CC1/2: 0.651 / % possible all: 88.2

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kml

3kml


Resolution: 3→48.97 Å / SU ML: 0.3313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.3397
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2888 2063 2.74 %
Rwork0.2688 73174 -
obs0.2694 75237 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.02 Å2
Refinement stepCycle: LAST / Resolution: 3→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18581 0 0 0 18581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001919006
X-RAY DIFFRACTIONf_angle_d0.451225942
X-RAY DIFFRACTIONf_chiral_restr0.03642975
X-RAY DIFFRACTIONf_plane_restr0.00323366
X-RAY DIFFRACTIONf_dihedral_angle_d7.731911220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.47421390.51614809X-RAY DIFFRACTION97.98
3.07-3.150.5221370.49184821X-RAY DIFFRACTION97.85
3.15-3.230.43971350.44524832X-RAY DIFFRACTION97.66
3.23-3.330.47291350.41314871X-RAY DIFFRACTION98.2
3.33-3.430.47611370.42384831X-RAY DIFFRACTION98.42
3.43-3.560.44461430.39464784X-RAY DIFFRACTION97.45
3.56-3.70.36021350.34854873X-RAY DIFFRACTION97.93
3.7-3.870.31921390.29514857X-RAY DIFFRACTION98.54
3.87-4.070.25751310.25184892X-RAY DIFFRACTION98.49
4.07-4.330.26061390.23884877X-RAY DIFFRACTION98.86
4.33-4.660.23381380.22044942X-RAY DIFFRACTION99.28
4.66-5.130.20031390.19644903X-RAY DIFFRACTION98.98
5.13-5.870.21381370.19614944X-RAY DIFFRACTION99.67
5.87-7.390.24881380.24034958X-RAY DIFFRACTION99.36
7.39-48.970.20431410.17254980X-RAY DIFFRACTION98.82

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