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- PDB-4y6x: Structure of Tobacco streak virus coat protein at 2.1 Angstroms r... -

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Basic information

Entry
Database: PDB / ID: 4y6x
TitleStructure of Tobacco streak virus coat protein at 2.1 Angstroms resolution (C2 crystal form)
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGulati, A. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DST, DBT, J.C 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / 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


Theoretical massNumber of molelcules
Total (without water)55,6003
Polymers55,6003
Non-polymers00
Water3,423190
1
A: Coat protein

A: Coat protein


Theoretical massNumber of molelcules
Total (without water)37,0672
Polymers37,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area2720 Å2
ΔGint-21 kcal/mol
Surface area14470 Å2
MethodPISA
2
B: Coat protein

B: Coat protein


Theoretical massNumber of molelcules
Total (without water)37,0672
Polymers37,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_457-x-1,y,-z+21
Buried area2640 Å2
ΔGint-24 kcal/mol
Surface area14840 Å2
MethodPISA
3
C: Coat protein

C: Coat protein


Theoretical massNumber of molelcules
Total (without water)37,0672
Polymers37,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area2160 Å2
ΔGint-21 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.580, 74.670, 85.500
Angle α, β, γ (deg.)90.000, 123.730, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA90 - 23718 - 165
21GLNGLNBB90 - 23718 - 165
12ASNASNAA90 - 23618 - 164
22ASNASNCC90 - 23618 - 164
13VALVALBB90 - 23518 - 163
23VALVALCC90 - 23518 - 163

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Coat protein


Mass: 18533.301 Da / Num. of mol.: 3 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 24% PEG 1500, 0.2 M L-Proline, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.2819 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2819 Å / Relative weight: 1
ReflectionResolution: 2.1→71.107 Å / Num. all: 27988 / Num. obs: 27988 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Rsym value: 0.067 / Net I/av σ(I): 8.822 / Net I/σ(I): 13.1 / Num. measured all: 114040
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.2140.47831608340300.2730.478399.5
2.21-2.354.10.3262.31557938450.1860.3264.299.6
2.35-2.514.10.2373.11483936300.1340.2375.699.8
2.51-2.714.10.164.61371733570.090.167.799.8
2.71-2.974.10.1017.31283431390.0570.10111.4100
2.97-3.324.10.06310.71157028110.0350.06318100
3.32-3.834.10.04514.91023424880.0250.04525.1100
3.83-4.74.10.03816.4875121190.0210.03830.4100
4.7-6.644.10.03716.5681016600.0210.03730.9100
6.64-28.93340.03415.136239090.0190.03431.699

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y6T

4y6t


Resolution: 2.1→28.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.1755 / FOM work R set: 0.851 / SU B: 4.845 / SU ML: 0.128 / SU R Cruickshank DPI: 0.1981 / SU Rfree: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1407 5 %RANDOM
Rwork0.178 ---
obs0.1806 26581 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.64 Å2 / Biso mean: 39.856 Å2 / Biso min: 17.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 190 3455
Biso mean---45.11 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023342
X-RAY DIFFRACTIONr_bond_other_d0.0070.023216
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9614549
X-RAY DIFFRACTIONr_angle_other_deg1.3637326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44422.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82815515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3391526
X-RAY DIFFRACTIONr_chiral_restr0.1070.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213751
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02775
X-RAY DIFFRACTIONr_mcbond_it3.8433.8491725
X-RAY DIFFRACTIONr_mcbond_other3.8223.8491724
X-RAY DIFFRACTIONr_mcangle_it5.5345.7462144
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73000.12
12B73000.12
21A71930.13
22C71930.13
31B70480.13
32C70480.13
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 116 -
Rwork0.247 1924 -
all-2040 -
obs--99.32 %

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