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- PDB-5bkq: Crystallographic structure of a cubic form of STMV grown from nitrate -

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Basic information

Entry
Database: PDB / ID: 5bkq
TitleCrystallographic structure of a cubic form of STMV grown from nitrate
ComponentsCoat protein
KeywordsVIRUS / ions / RNA / decapsidation / ion channel / crystallization
Function / homologySatellite virus coat domain superfamily / viral capsid / structural molecule activity / NITRATE ION / Coat protein
Function and homology information
Biological speciesSatellite tobacco mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 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 21, 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
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,222131
Polymers350,67920
Non-polymers6,543111
Water28,5181583
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
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
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
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
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
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,071,667393
Polymers1,052,03760
Non-polymers19,630333
Water1,08160
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)234.050, 234.050, 234.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
Components on special symmetry positions
IDModelComponents
11L-505-

NO3

21L-506-

NO3

31L-508-

NO3

41HH-303-

NO3

51D-446-

HOH

61D-453-

HOH

71E-536-

HOH

81E-539-

HOH

91J-1049-

HOH

101J-1072-

HOH

111J-1081-

HOH

121L-613-

HOH

131M-643-

HOH

141M-652-

HOH

151JJ-322-

HOH

161JJ-335-

HOH

171KK-353-

HOH

181KK-358-

HOH

191KK-366-

HOH

201KK-368-

HOH

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Components

#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
#2: Chemical...
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 102 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1583 / Source method: isolated from a natural source / Formula: H2O
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: 3.05 Å3/Da / Density % sol: 59.63 % / Description: 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. Drops were equal amounts of a 5 mg/ml virus stock solution buffered with 0.1 M phosphate at pH ...Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. Drops were equal amounts of a 5 mg/ml virus stock solution buffered with 0.1 M phosphate at pH 6.5, and the reservoir solution which was 20% w/v sodium nitrate in 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 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→105 Å / Num. obs: 45796 / % possible obs: 0.65 % / Redundancy: 3.8 % / Biso Wilson estimate: 50.45 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.143 / Rsym value: 0.142 / Net I/σ(I): 11.5
Reflection shellResolution: 3.18→3.25 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6489 / CC1/2: 0.46

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Processing

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

4oq8


Resolution: 3.19→75 Å / SU ML: 0.459 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.7232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2732 1923 4.99 %
Rwork0.2608 43507 -
obs0.2627 45793 64.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.84 Å2
Refinement stepCycle: LAST / Resolution: 3.19→75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22980 0 417 1583 24980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002624229
X-RAY DIFFRACTIONf_angle_d0.484933010
X-RAY DIFFRACTIONf_chiral_restr0.04673813
X-RAY DIFFRACTIONf_plane_restr0.00444378
X-RAY DIFFRACTIONf_dihedral_angle_d10.12318842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.260.3147620.31081078X-RAY DIFFRACTION25.69
3.26-3.330.3886620.30471072X-RAY DIFFRACTION25.65
3.33-3.420.3901550.29581085X-RAY DIFFRACTION25.96
3.42-3.510.3092470.29351053X-RAY DIFFRACTION24.94
3.51-3.610.2857610.31041123X-RAY DIFFRACTION26.56
3.61-3.730.3086840.2631504X-RAY DIFFRACTION36.16
3.73-3.860.2781120.27772012X-RAY DIFFRACTION48.02
3.86-4.020.32881270.26452677X-RAY DIFFRACTION63.1
4.02-4.20.29421510.2563199X-RAY DIFFRACTION75.62
4.2-4.420.26561640.24633668X-RAY DIFFRACTION86.02
4.42-4.70.27812180.22033880X-RAY DIFFRACTION92.55
4.7-5.060.2542270.22764107X-RAY DIFFRACTION96.87
5.06-5.570.29742530.25944168X-RAY DIFFRACTION99.04
5.57-6.370.28122100.25924280X-RAY DIFFRACTION99.78
6.37-8.030.33172310.2884266X-RAY DIFFRACTION100
8.03-104.670.33172220.27574335X-RAY DIFFRACTION97.6
Refinement TLS params.Method: refined / Origin x: 90.5462985363 Å / Origin y: 176.128540856 Å / Origin z: 29.0504143514 Å
111213212223313233
T0.226508248702 Å2-0.0631907518218 Å20.0321335484678 Å2-0.224036124755 Å20.0370009329029 Å2--0.118440765018 Å2
L-0.00535441898296 °2-0.0549884436878 °20.118753417903 °2--0.289635504512 °2-0.159811705408 °2--0.0998133393518 °2
S-0.0112799322219 Å °0.168435869142 Å °0.0385502455611 Å °-0.224206258604 Å °0.0800520032759 Å °-0.214330826166 Å °-0.0877913610759 Å °0.150240120728 Å °-0.00212507721122 Å °
Refinement TLS groupSelection details: all

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