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- PDB-4y5z: T=1 capsid structure of SeMV Ndel65CP fused with B-domain of S. a... -

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Basic information

Entry
Database: PDB / ID: 4y5z
TitleT=1 capsid structure of SeMV Ndel65CP fused with B-domain of S. aureus protein SpA at the N-terminus (P1 crystal form)
ComponentsImmunoglobulin G-binding protein A,Coat protein
KeywordsVIRUS / coat protein / chimeric VLP / in vitro assembly
Function / homology
Function and homology information


IgG binding / viral capsid / structural molecule activity / extracellular region / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain ...Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / Jelly Rolls - #20 / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Capsid protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Sesbania mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGulati, A. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DST, DBT, J.C Bose India
CitationJournal: Virology / Year: 2015
Title: Structural studies on chimeric Sesbania mosaic virus coat protein: Revisiting SeMV assembly.
Authors: Gulati, A. / Murthy, A. / Abraham, A. / Mohan, K. / Natraj, U. / Savithri, H.S. / Murthy, M.R.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein A,Coat protein
B: Immunoglobulin G-binding protein A,Coat protein
C: Immunoglobulin G-binding protein A,Coat protein
D: Immunoglobulin G-binding protein A,Coat protein
E: Immunoglobulin G-binding protein A,Coat protein
F: Immunoglobulin G-binding protein A,Coat protein
G: Immunoglobulin G-binding protein A,Coat protein
H: Immunoglobulin G-binding protein A,Coat protein
I: Immunoglobulin G-binding protein A,Coat protein
J: Immunoglobulin G-binding protein A,Coat protein
K: Immunoglobulin G-binding protein A,Coat protein
L: Immunoglobulin G-binding protein A,Coat protein
M: Immunoglobulin G-binding protein A,Coat protein
N: Immunoglobulin G-binding protein A,Coat protein
O: Immunoglobulin G-binding protein A,Coat protein
P: Immunoglobulin G-binding protein A,Coat protein
Q: Immunoglobulin G-binding protein A,Coat protein
R: Immunoglobulin G-binding protein A,Coat protein
S: Immunoglobulin G-binding protein A,Coat protein
T: Immunoglobulin G-binding protein A,Coat protein
U: Immunoglobulin G-binding protein A,Coat protein
V: Immunoglobulin G-binding protein A,Coat protein
W: Immunoglobulin G-binding protein A,Coat protein
X: Immunoglobulin G-binding protein A,Coat protein
Y: Immunoglobulin G-binding protein A,Coat protein
Z: Immunoglobulin G-binding protein A,Coat protein
a: Immunoglobulin G-binding protein A,Coat protein
c: Immunoglobulin G-binding protein A,Coat protein
e: Immunoglobulin G-binding protein A,Coat protein
g: Immunoglobulin G-binding protein A,Coat protein
i: Immunoglobulin G-binding protein A,Coat protein
k: Immunoglobulin G-binding protein A,Coat protein
m: Immunoglobulin G-binding protein A,Coat protein
o: Immunoglobulin G-binding protein A,Coat protein
q: Immunoglobulin G-binding protein A,Coat protein
r: Immunoglobulin G-binding protein A,Coat protein
s: Immunoglobulin G-binding protein A,Coat protein
t: Immunoglobulin G-binding protein A,Coat protein
u: Immunoglobulin G-binding protein A,Coat protein
v: Immunoglobulin G-binding protein A,Coat protein
w: Immunoglobulin G-binding protein A,Coat protein
x: Immunoglobulin G-binding protein A,Coat protein
y: Immunoglobulin G-binding protein A,Coat protein
z: Immunoglobulin G-binding protein A,Coat protein
0: Immunoglobulin G-binding protein A,Coat protein
1: Immunoglobulin G-binding protein A,Coat protein
2: Immunoglobulin G-binding protein A,Coat protein
3: Immunoglobulin G-binding protein A,Coat protein
4: Immunoglobulin G-binding protein A,Coat protein
5: Immunoglobulin G-binding protein A,Coat protein
6: Immunoglobulin G-binding protein A,Coat protein
7: Immunoglobulin G-binding protein A,Coat protein
b: Immunoglobulin G-binding protein A,Coat protein
d: Immunoglobulin G-binding protein A,Coat protein
f: Immunoglobulin G-binding protein A,Coat protein
h: Immunoglobulin G-binding protein A,Coat protein
j: Immunoglobulin G-binding protein A,Coat protein
l: Immunoglobulin G-binding protein A,Coat protein
n: Immunoglobulin G-binding protein A,Coat protein
p: Immunoglobulin G-binding protein A,Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,833,74672
Polymers1,832,59360
Non-polymers1,15312
Water26,1401451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area241070 Å2
ΔGint-1223 kcal/mol
Surface area304840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.480, 187.420, 187.930
Angle α, β, γ (deg.)61.090, 89.240, 60.200
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
271
281
291
301

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B
311chain C
411chain D
511chain E
611chain F
711chain G
811chain H
911chain I
1011chain J
1111chain K
1211chain L
1311chain M
1411chain N
1511chain O
1611chain P
1711chain Q
1811chain R
1911chain S
2011chain T
2111chain U
2211chain V
2311chain W
2411chain X
2511chain Y
2611chain Z
2711chain a
2811chain b
2911chain c
3011chain d

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Components

#1: Antibody ...
Immunoglobulin G-binding protein A,Coat protein / IgG-binding protein A / Staphylococcal protein A


Mass: 30543.213 Da / Num. of mol.: 60 / Fragment: UNP RESIDUES 158-211,UNP RESIDUES 66-268
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF SPA (158-211), LINKER, AND COAT PROTEIN (66-268)
Source: (gene. exp.) Staphylococcus aureus (bacteria), (gene. exp.) Sesbania mosaic virus
Strain: NCTC 8325 / Gene: spa, SAOUHSC_00069 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P02976, UniProt: Q9EB06
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1451 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15-25% PEG 400, 0.2M magnesium chloride, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.95→41.92 Å / Num. all: 365689 / Num. obs: 365689 / % possible obs: 94.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.83 Å2 / Rpim(I) all: 0.092 / Rrim(I) all: 0.176 / Rsym value: 0.149 / Net I/av σ(I): 4.649 / Net I/σ(I): 6.6 / Num. measured all: 1255405
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
2.95-3.112.70.4692.2131461484410.3150.4692.285.2
3.11-3.32.80.3172.4135868478670.2120.3173.289.1
3.3-3.533.10.2273.3143433467780.1490.2274.592.6
3.53-3.813.40.1644.4152862452020.1040.1646.596.3
3.81-4.173.70.145157534423230.0840.147.997.9
4.17-4.663.90.116.1150954383720.0640.119.898.3
4.66-5.3940.1036.6134839339140.0590.1031098.4
5.39-6.640.1136113963286430.0650.1138.798.6
6.6-9.3340.096.587732221800.0530.0910.198.7
9.33-41.9163.90.0776.646759119690.0450.07711.797.5

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VAK

1vak


Resolution: 2.95→41.916 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 18383 5.03 %Random selection
Rwork0.196 347223 --
obs0.1987 365606 94.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.93 Å2 / Biso mean: 27.2502 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.95→41.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms85411 0 60 1451 86922
Biso mean--11.86 20.67 -
Num. residues----11534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0187439
X-RAY DIFFRACTIONf_angle_d1.255119808
X-RAY DIFFRACTIONf_chiral_restr0.05514521
X-RAY DIFFRACTIONf_plane_restr0.00814704
X-RAY DIFFRACTIONf_dihedral_angle_d11.34829578
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A51669X-RAY DIFFRACTION6.921TORSIONAL
12B51669X-RAY DIFFRACTION6.921TORSIONAL
13C51669X-RAY DIFFRACTION6.921TORSIONAL
14D51669X-RAY DIFFRACTION6.921TORSIONAL
15E51669X-RAY DIFFRACTION6.921TORSIONAL
16F51669X-RAY DIFFRACTION6.921TORSIONAL
17G51669X-RAY DIFFRACTION6.921TORSIONAL
18H51669X-RAY DIFFRACTION6.921TORSIONAL
19I51669X-RAY DIFFRACTION6.921TORSIONAL
110J51669X-RAY DIFFRACTION6.921TORSIONAL
111K51669X-RAY DIFFRACTION6.921TORSIONAL
112L51669X-RAY DIFFRACTION6.921TORSIONAL
113M51669X-RAY DIFFRACTION6.921TORSIONAL
114N51669X-RAY DIFFRACTION6.921TORSIONAL
115O51669X-RAY DIFFRACTION6.921TORSIONAL
116P51669X-RAY DIFFRACTION6.921TORSIONAL
117Q51669X-RAY DIFFRACTION6.921TORSIONAL
118R51669X-RAY DIFFRACTION6.921TORSIONAL
119S51669X-RAY DIFFRACTION6.921TORSIONAL
120T51669X-RAY DIFFRACTION6.921TORSIONAL
121U51669X-RAY DIFFRACTION6.921TORSIONAL
122V51669X-RAY DIFFRACTION6.921TORSIONAL
123W51669X-RAY DIFFRACTION6.921TORSIONAL
124X51669X-RAY DIFFRACTION6.921TORSIONAL
125Y51669X-RAY DIFFRACTION6.921TORSIONAL
126Z51669X-RAY DIFFRACTION6.921TORSIONAL
127a51669X-RAY DIFFRACTION6.921TORSIONAL
128b51669X-RAY DIFFRACTION6.921TORSIONAL
129c51669X-RAY DIFFRACTION6.921TORSIONAL
130d51669X-RAY DIFFRACTION6.921TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-2.98350.35435430.2789104311097484
2.9835-3.01860.33015330.2804104711100485
3.0186-3.05540.33425300.2638104381096885
3.0554-3.09410.30856050.254105391114486
3.0941-3.13480.3215490.2519107741132387
3.1348-3.17770.32195930.2542109091150289
3.1777-3.22310.30675610.2671108221138388
3.2231-3.27120.31795670.2443110791164690
3.2712-3.32230.29425660.2448112181178491
3.3223-3.37670.29215700.2332111991176991
3.3767-3.43490.29836040.2275113971200193
3.4349-3.49730.26226640.2148115291219394
3.4973-3.56460.2796140.2117116761229095
3.5646-3.63730.26086240.2065117911241596
3.6373-3.71630.26226120.2028118471245996
3.7163-3.80270.23946220.1838119751259797
3.8027-3.89780.23256830.1758119931267698
3.8978-4.00310.23566240.1835120211264598
4.0031-4.12080.22516570.1729119961265398
4.1208-4.25360.23416430.1689121301277398
4.2536-4.40550.1996210.1599119891261098
4.4055-4.58170.20486140.1503121931280798
4.5817-4.78990.20556830.159120601274398
4.7899-5.04210.20766360.1589120941273098
5.0421-5.35740.21326300.1678121421277299
5.3574-5.77010.2216580.1703120491270799
5.7701-6.3490.22526280.174121231275199
6.349-7.26350.22386560.1772121131276999
7.2635-9.13570.20596590.1731121081276799
9.1357-41.920.26046340.2095121171275198

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