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- PDB-3kml: Circular Permutant of the Tobacco Mosaic Virus -

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Basic information

Entry
Database: PDB / ID: 3kml
TitleCircular Permutant of the Tobacco Mosaic Virus
ComponentsCoat protein
KeywordsVIRAL PROTEIN / tobacco mosaic virus coat protein / permutant / TMV / TMVP / cpTMVP / Acetylation / Capsid protein / Virion
Function / homology
Function and homology information


helical viral capsid / structural molecule activity / identical protein binding
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #190 / Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesTobacco mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.011 Å
AuthorsDuderstadt, K.E. / Dedeo, M.T. / Francis, M.B. / Berger, J.M.
CitationJournal: Nano Lett. / Year: 2010
Title: Nanoscale protein assemblies from a circular permutant of the tobacco mosaic virus.
Authors: Dedeo, M.T. / Duderstadt, K.E. / Berger, J.M. / Francis, M.B.
History
DepositionNov 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: Coat protein
Q: Coat protein


Theoretical massNumber of molelcules
Total (without water)301,25117
Polymers301,25117
Non-polymers00
Water00
1
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: Coat protein
Q: Coat protein

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


Theoretical massNumber of molelcules
Total (without water)602,50234
Polymers602,50234
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area86420 Å2
ΔGint-285 kcal/mol
Surface area189630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.835, 177.175, 102.801
Angle α, β, γ (deg.)90.00, 99.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 13 - 153 / Label seq-ID: 13 - 153

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 13:153 )AA
2chain B and (resseq 13:153 )BB
3chain C and (resseq 13:153 )CC
4chain D and (resseq 13:153 )DD
5chain E and (resseq 13:153 )EE
6chain F and (resseq 13:153 )FF
7chain G and (resseq 13:153 )GG
8chain H and (resseq 13:153 )HH
9chain I and (resseq 13:153 )II
10chain J and (resseq 13:153 )JJ
11chain K and (resseq 13:153 )KK
12chain L and (resseq 13:153 )LL
13chain M and (resseq 13:153 )MM
14chain N and (resseq 13:153 )NN
15chain O and (resseq 13:153 )OO
16chain P and (resseq 13:153 )PP
17chain Q and (resseq 13:153 )QQ

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Components

#1: Protein
Coat protein


Mass: 17720.654 Da / Num. of mol.: 17 / Mutation: S25C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco mosaic virus / Strain: U1 / Gene: CP / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner DE3pLysS cells / 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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 300 mM ammonium sulfate, 100 mM Nitric Acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 73255 / % possible obs: 94.8 % / Redundancy: 3 % / Biso Wilson estimate: 29.65 Å2 / Rsym value: 0.116 / Net I/σ(I): 7.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.447 / % possible all: 81.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementStarting model: One ring of 17 monomers generated using PDB ID 1EI7.

1ei7


Resolution: 3.011→49.261 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.806 / SU ML: 0.39 / σ(F): 0.06 / Phase error: 26.46 / Stereochemistry target values: ML
Details: Used 17-fold non-crystallographic symmetry as a constraint during refinement.
RfactorNum. reflection% reflection
Rfree0.253 1629 2.7 %
Rwork0.239 58611 -
obs0.24 60240 78.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.001 Å2 / ksol: 0.298 e/Å3
Displacement parametersBiso max: 178.95 Å2 / Biso mean: 42.997 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1--3.824 Å20 Å2-23.358 Å2
2---24.197 Å2-0 Å2
3---19.324 Å2
Refinement stepCycle: LAST / Resolution: 3.011→49.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18700 0 0 0 18700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419108
X-RAY DIFFRACTIONf_angle_d0.93526078
X-RAY DIFFRACTIONf_dihedral_angle_d15.4866732
X-RAY DIFFRACTIONf_chiral_restr0.0432992
X-RAY DIFFRACTIONf_plane_restr0.0133400
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1100X-RAY DIFFRACTIONPOSITIONAL
12B1100X-RAY DIFFRACTIONPOSITIONAL0
13C1100X-RAY DIFFRACTIONPOSITIONAL0.001
14D1100X-RAY DIFFRACTIONPOSITIONAL0
15E1100X-RAY DIFFRACTIONPOSITIONAL0
16F1100X-RAY DIFFRACTIONPOSITIONAL0.001
17G1100X-RAY DIFFRACTIONPOSITIONAL0
18H1100X-RAY DIFFRACTIONPOSITIONAL0.001
19I1100X-RAY DIFFRACTIONPOSITIONAL0
110J1100X-RAY DIFFRACTIONPOSITIONAL0
111K1100X-RAY DIFFRACTIONPOSITIONAL0.001
112L1100X-RAY DIFFRACTIONPOSITIONAL0.001
113M1100X-RAY DIFFRACTIONPOSITIONAL0.001
114N1100X-RAY DIFFRACTIONPOSITIONAL0
115O1100X-RAY DIFFRACTIONPOSITIONAL0
116P1100X-RAY DIFFRACTIONPOSITIONAL0.001
117Q1100X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0111-3.09960.399910.35633527X-RAY DIFFRACTION57
3.0996-3.19970.34411040.31154139X-RAY DIFFRACTION66
3.1997-3.3140.31571180.29664290X-RAY DIFFRACTION69
3.314-3.44670.30861420.27764652X-RAY DIFFRACTION75
3.4467-3.60350.25871420.26684924X-RAY DIFFRACTION79
3.6035-3.79340.27411480.26525283X-RAY DIFFRACTION85
3.7934-4.0310.22791350.20584890X-RAY DIFFRACTION78
4.031-4.3420.20921340.19794813X-RAY DIFFRACTION77
4.342-4.77870.20461310.18025031X-RAY DIFFRACTION81
4.7787-5.46940.16891590.16685432X-RAY DIFFRACTION87
5.4694-6.88780.20241550.21875553X-RAY DIFFRACTION88
6.8878-49.26720.22441700.21196077X-RAY DIFFRACTION96

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