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- PDB-4y6t: Structure of Tobacco streak virus coat protein dimer at 2.4 Angst... -

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Basic information

Entry
Database: PDB / ID: 4y6t
TitleStructure of Tobacco streak virus coat protein dimer at 2.4 Angstroms resolution
ComponentsCoat protein
KeywordsSTRUCTURAL PROTEIN / domain-swapped dimer / jelly roll beta-barrel
Function / homologyCoat protein, Ilarvirus, predicted / Coat protein, Ilarvirus / Ilarvirus coat protein / viral capsid / RNA binding / Coat protein
Function and homology information
Biological speciesTobacco streak virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsGulati, A. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DST, DBT, JC Bose India
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structural studies on tobacco streak virus coat protein: Insights into the pleomorphic nature of ilarviruses
Authors: Gulati, A. / Alapati, K. / Murthy, A. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7197
Polymers111,6576
Non-polymers621
Water7,692427
1
A: Coat protein
F: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2813
Polymers37,2192
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-14 kcal/mol
Surface area15160 Å2
MethodPISA
2
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)37,2192
Polymers37,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-19 kcal/mol
Surface area15160 Å2
MethodPISA
3
D: Coat protein
E: Coat protein


Theoretical massNumber of molelcules
Total (without water)37,2192
Polymers37,2192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-18 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.040, 69.980, 103.440
Angle α, β, γ (deg.)90.000, 105.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA90 - 23818 - 166
21SERSERBB90 - 23818 - 166
12LEULEUAA91 - 23819 - 166
22LEULEUCC91 - 23819 - 166
13LEULEUAA91 - 23819 - 166
23LEULEUDD91 - 23819 - 166
14SERSERAA90 - 23818 - 166
24SERSEREE90 - 23818 - 166
15SERSERAA90 - 23818 - 166
25SERSERFF90 - 23818 - 166
16LEULEUBB91 - 23819 - 166
26LEULEUCC91 - 23819 - 166
17LEULEUBB91 - 23819 - 166
27LEULEUDD91 - 23819 - 166
18SERSERBB90 - 23818 - 166
28SERSEREE90 - 23818 - 166
19SERSERBB90 - 23818 - 166
29SERSERFF90 - 23818 - 166
110LEULEUCC91 - 23819 - 166
210LEULEUDD91 - 23819 - 166
111LEULEUCC91 - 23819 - 166
211LEULEUEE91 - 23819 - 166
112LEULEUCC91 - 23819 - 166
212LEULEUFF91 - 23819 - 166
113LEULEUDD91 - 23819 - 166
213LEULEUEE91 - 23819 - 166
114LEULEUDD91 - 23819 - 166
214LEULEUFF91 - 23819 - 166
115SERSEREE90 - 23818 - 166
215SERSERFF90 - 23818 - 166

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Coat protein


Mass: 18609.418 Da / Num. of mol.: 6 / Fragment: UNP residues 73-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco streak virus / Production host: Escherichia coli (E. coli) / References: UniProt: A7UMQ4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 3.22 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 8000, 10% glycerol, 0.5M potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2013
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.4→99.673 Å / Num. all: 54445 / Num. obs: 54445 / % possible obs: 97.8 % / Redundancy: 7.8 % / Rpim(I) all: 0.036 / Rrim(I) all: 0.101 / Rsym value: 0.095 / Net I/av σ(I): 7.422 / Net I/σ(I): 16.3 / Num. measured all: 422296
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.537.80.6923.26103578220.2640.6923.297.2
2.53-2.687.80.4791.65811474480.1830.4794.597.4
2.68-2.877.80.3072.55471470180.1170.3076.797.5
2.87-3.17.80.18945108565520.0720.18910.297.8
3.1-3.397.80.116.84700260340.0420.1116.697.9
3.39-3.797.80.0759.54286155160.0290.07523.998.1
3.79-4.387.70.05512.43758748640.0210.05530.498.3
4.38-5.377.70.04315.33189241400.0170.04336.498.5
5.37-7.597.60.04514.22469432340.0170.04533.298.7
7.59-40.347.30.03417.31331218170.0130.03440.797.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→99.67 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.084 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 2765 5.1 %RANDOM
Rwork0.2075 ---
obs0.2093 51665 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.62 Å2 / Biso mean: 47.479 Å2 / Biso min: 14.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.4→99.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6695 0 4 427 7126
Biso mean--27.59 42.23 -
Num. residues----868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026881
X-RAY DIFFRACTIONr_bond_other_d0.0090.026436
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9639370
X-RAY DIFFRACTIONr_angle_other_deg1.492314729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6145859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8823.576302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.394151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0721555
X-RAY DIFFRACTIONr_chiral_restr0.0990.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217803
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021572
X-RAY DIFFRACTIONr_mcbond_it4.4184.7433472
X-RAY DIFFRACTIONr_mcbond_other4.4114.7433471
X-RAY DIFFRACTIONr_mcangle_it6.6247.0864319
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A72270.11
12B72270.11
21A74820.11
22C74820.11
31A75610.11
32D75610.11
41A78190.11
42E78190.11
51A71340.1
52F71340.1
61B73650.09
62C73650.09
71B73480.09
72D73480.09
81B73280.1
82E73280.1
91B69020.1
92F69020.1
101C75640.09
102D75640.09
111C77010.09
112E77010.09
121C69570.1
122F69570.1
131D78200.09
132E78200.09
141D71580.1
142F71580.1
151E71780.1
152F71780.1
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 199 -
Rwork0.287 3753 -
all-3952 -
obs--96.98 %

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