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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 / T=3 icosahedral viral capsid / translational initiation / viral nucleocapsid / ribonucleoprotein complex / RNA binding / Capsid 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

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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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A90 - 238
2010B90 - 238
1020A91 - 238
2020C91 - 238
1030A91 - 238
2030D91 - 238
1040A90 - 238
2040E90 - 238
1050A90 - 238
2050F90 - 238
1060B91 - 238
2060C91 - 238
1070B91 - 238
2070D91 - 238
1080B90 - 238
2080E90 - 238
1090B90 - 238
2090F90 - 238
10100C91 - 238
20100D91 - 238
10110C91 - 238
20110E91 - 238
10120C91 - 238
20120F91 - 238
10130D91 - 238
20130E91 - 238
10140D91 - 238
20140F91 - 238
10150E90 - 238
20150F90 - 238

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

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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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