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- PDB-5bkl: Crystallographic structure of the cubic crystal form of STMV (77.... -

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Basic information

Entry
Database: PDB / ID: 5bkl
TitleCrystallographic structure of the cubic crystal form of STMV (77.9 degree rotation) grown from NaCl
Components
  • Coat protein
  • RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRUS/RNA / VIRUS-RNA complex
Function / homologySatellite virus coat domain superfamily / viral capsid / structural molecule activity / RNA / RNA (> 10) / Coat protein
Function and homology information
Biological speciesSatellite tobacco mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.
Authors: McPherson, A.
History
DepositionMar 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,28592
Polymers423,55139
Non-polymers1,73453
Water16,484915
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: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules

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: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules

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: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,275,855276
Polymers1,270,653117
Non-polymers5,202159
Water2,108117
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Unit cell
Length a, b, c (Å)234.650, 234.650, 234.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Components on special symmetry positions
IDModelComponents
11C-309-

HOH

21M-207-

HOH

31M-212-

HOH

41M-216-

HOH

51O-244-

HOH

61e-238-

HOH

71II-359-

HOH

81JJ-452-

HOH

91JJ-453-

HOH

101JJ-454-

HOH

111KK-335-

HOH

121KK-346-

HOH

131KK-350-

HOH

141KK-354-

HOH

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Components

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Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOGGHHIIJJKK

#1: Protein
Coat protein


Mass: 17533.949 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Satellite tobacco mosaic virus / References: UniProt: P17574

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RNA chain , 4 types, 19 molecules PSTVXUUbbYaTTehinWWkkllqqm

#2: RNA chain
RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3905.512 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide dodecamer / Source: (natural) Satellite tobacco mosaic virus
#3: RNA chain RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3576.306 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide undecamer / Source: (natural) Satellite tobacco mosaic virus
#4: RNA chain
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3935.198 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide tridecamer / Source: (natural) Satellite tobacco mosaic virus
#5: RNA chain RNA (5'-R(UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3322.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide undecamer / Source: (natural) Satellite tobacco mosaic virus

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Non-polymers , 3 types, 968 molecules

#6: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 915 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.61 % / Description: large octahedra
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were composed of equal amounts of a 5 mg/ml stock virus solution buffered at pH6.5 ...Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were composed of equal amounts of a 5 mg/ml stock virus solution buffered at pH6.5 with 0.1 M phosphate, and the reservoir solution which was 8% w/v NaCl buffered with 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.
PH range: 4.5 - 7.0

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→100.5 Å / Num. obs: 87022 / % possible obs: 96 % / Redundancy: 7.8 % / Biso Wilson estimate: 43.85 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.17 / Rsym value: 0.15 / Net I/σ(I): 7.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 8458 / CC1/2: 0.52 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQ8

4oq8


Resolution: 2.94→78.22 Å / SU ML: 0.3568 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 4392 5.05 %
Rwork0.2168 82524 -
obs0.2187 86916 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.43 Å2
Refinement stepCycle: LAST / Resolution: 2.94→78.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22546 2926 53 915 26440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003526751
X-RAY DIFFRACTIONf_angle_d0.715337148
X-RAY DIFFRACTIONf_chiral_restr0.06164445
X-RAY DIFFRACTIONf_plane_restr0.0124340
X-RAY DIFFRACTIONf_dihedral_angle_d13.635910281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-2.980.34951350.31792613X-RAY DIFFRACTION90.39
2.98-3.010.33991460.33822526X-RAY DIFFRACTION90.12
3.01-3.050.33041320.29652663X-RAY DIFFRACTION91.46
3.05-3.090.35111350.30032568X-RAY DIFFRACTION91.23
3.09-3.130.33941420.28732674X-RAY DIFFRACTION91.64
3.13-3.170.33441430.27382620X-RAY DIFFRACTION92.47
3.17-3.210.28061340.27792705X-RAY DIFFRACTION93.88
3.22-3.260.30281460.2752621X-RAY DIFFRACTION93.61
3.26-3.310.29731440.26282707X-RAY DIFFRACTION94.31
3.31-3.370.27881310.24882710X-RAY DIFFRACTION94.39
3.37-3.430.29191640.24142701X-RAY DIFFRACTION94.65
3.43-3.490.28851460.23692735X-RAY DIFFRACTION95.46
3.49-3.560.27511520.242728X-RAY DIFFRACTION95.3
3.56-3.630.25181330.22042742X-RAY DIFFRACTION95.67
3.63-3.710.28851450.23182759X-RAY DIFFRACTION95.78
3.71-3.790.24651390.21752768X-RAY DIFFRACTION96.39
3.79-3.890.26121620.21852765X-RAY DIFFRACTION96.89
3.89-3.990.24751580.20262795X-RAY DIFFRACTION96.95
3.99-4.110.23511550.19092769X-RAY DIFFRACTION97.6
4.11-4.240.25671440.19012846X-RAY DIFFRACTION97.65
4.24-4.390.22721390.17862797X-RAY DIFFRACTION98
4.4-4.570.19621550.16182836X-RAY DIFFRACTION98
4.57-4.780.21831400.16632852X-RAY DIFFRACTION98
4.78-5.030.19641410.16142838X-RAY DIFFRACTION98.06
5.03-5.340.22421590.18662830X-RAY DIFFRACTION98.06
5.35-5.760.22851420.19922872X-RAY DIFFRACTION98.27
5.76-6.340.23911670.20272821X-RAY DIFFRACTION97.74
6.34-7.250.28371500.22162851X-RAY DIFFRACTION97.69
7.26-9.130.21711420.19492911X-RAY DIFFRACTION98.01
9.14-78.220.2251710.20412901X-RAY DIFFRACTION95.23
Refinement TLS params.Method: refined / Origin x: 86.0738547588 Å / Origin y: 171.966525204 Å / Origin z: 26.5275741109 Å
111213212223313233
T0.12186591289 Å20.0878223498826 Å2-0.0319498374984 Å2-0.229290314962 Å2-0.0157560837212 Å2--0.329619356447 Å2
L0.0974549762657 °20.00909854200297 °2-0.0461760167651 °2-0.0998404197396 °20.0621215706241 °2--0.117133193903 °2
S-0.0398863062551 Å °-0.0455784402528 Å °-0.117749386616 Å °0.010732897789 Å °0.0636464959339 Å °-0.2122347697 Å °0.0809150086577 Å °0.155304469239 Å °0.00321586047534 Å °
Refinement TLS groupSelection details: all

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