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- PDB-7m3r: Crystallographic Structure of the Rhombohedral Crystal Form of ST... -

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Basic information

Entry
Database: PDB / ID: 7m3r
TitleCrystallographic Structure of the Rhombohedral Crystal Form of STMV Grown from Bromide
ComponentsCoat protein
KeywordsVIRUS / halide / RNA / twinning / absence / bromide ions / axis ions / ion channel / decapsidation
Function / homologySatellite virus coat domain superfamily / viral capsid / structural molecule activity / BROMIDE ION / Coat protein
Function and homology information
Biological speciesSatellite tobacco mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 18, 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 1.2Oct 18, 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)366,135219
Polymers350,67920
Non-polymers15,456199
Water80,4374465
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)1,098,405657
Polymers1,052,03760
Non-polymers46,368597
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)166.491, 166.491, 435.839
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11N-1303-

BR

21GG-213-

BR

31GG-216-

BR

41GG-217-

BR

51B-511-

HOH

61D-563-

HOH

71D-601-

HOH

81D-616-

HOH

91D-620-

HOH

101F-824-

HOH

111H-532-

HOH

121H-559-

HOH

131H-583-

HOH

141K-542-

HOH

151M-631-

HOH

161M-713-

HOH

171M-814-

HOH

181N-1506-

HOH

191N-1555-

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-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 191 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 4465 / 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: 3.32 Å3/Da / Density % sol: 62.9 %
Description: Apex truncated triangular plates very similar in appearance to the monoclinic crystal form and the rhombohedral crystal form grown from chloride.
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs and 6 to 8 ul drops. The drops were equal amounts of a 5 mg/ml virus stock solution buffered at ...Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs and 6 to 8 ul drops. The drops were equal amounts of a 5 mg/ml virus stock solution buffered at pH 6.5 with 0.1 M phosphate. The reservoirs were 5% w/v NaBr in 0.1 M phosphate at pH 6.0. Crystallization was at 4 degrees C and the time of development was about 10 days.
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 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→55 Å / Num. obs: 200162 / % possible obs: 86 % / Redundancy: 4.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.16 / Rsym value: 0.15 / Net I/σ(I): 4.5
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 13000 / CC1/2: 0.44 / % possible all: 35

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Processing

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

4oq8


Resolution: 2.1→54.08 Å / Cross valid method: FREE R-VALUE / σ(F): 233.96 / Phase error: 22.0814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2082 10048 5.69 %
Rwork0.171 188122 -
obs0.1805 199466 76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→54.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22605 0 199 4465 27269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002923321
X-RAY DIFFRACTIONf_angle_d0.481131853
X-RAY DIFFRACTIONf_chiral_restr0.04833719
X-RAY DIFFRACTIONf_plane_restr0.00534156
X-RAY DIFFRACTIONf_dihedral_angle_d10.23258541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.29371780.23563343X-RAY DIFFRACTION25.54
2.14-2.180.26741800.23193800X-RAY DIFFRACTION29.02
2.18-2.220.28812130.26373940X-RAY DIFFRACTION29.92
2.22-2.260.30182510.21734689X-RAY DIFFRACTION35.78
2.26-2.310.31283030.25055775X-RAY DIFFRACTION44.02
2.31-2.370.29223400.2276715X-RAY DIFFRACTION51.32
2.37-2.430.24714400.2057740X-RAY DIFFRACTION58.77
2.43-2.490.24115240.18948849X-RAY DIFFRACTION67.36
2.49-2.560.25135010.189510064X-RAY DIFFRACTION76.6
2.56-2.650.2415730.1811085X-RAY DIFFRACTION84.5
2.65-2.740.22586660.175111758X-RAY DIFFRACTION89.54
2.74-2.850.21976070.174512130X-RAY DIFFRACTION92.91
2.85-2.980.21335950.1712469X-RAY DIFFRACTION94.73
2.98-3.140.22866480.176212393X-RAY DIFFRACTION94.74
3.14-3.340.22166790.176812462X-RAY DIFFRACTION94.7
3.34-3.590.20796200.175712464X-RAY DIFFRACTION95.13
3.59-3.950.20726470.168512548X-RAY DIFFRACTION95.05
3.95-4.530.16366800.148912385X-RAY DIFFRACTION94.64
4.53-5.70.16866870.145612394X-RAY DIFFRACTION94.69
5.7-54.080.23896770.227312454X-RAY DIFFRACTION94.58
Refinement TLS params.Method: refined / Origin x: 25.7088582164 Å / Origin y: 35.5795839466 Å / Origin z: 8.2450827742 Å
111213212223313233
T0.0914820428572 Å20.00254080047937 Å20.0022625119476 Å2-0.0867445354979 Å2-0.00263641389483 Å2--0.180935328076 Å2
L-0.0657962357378 °20.0223965192784 °20.0509379288006 °2--0.0530161991873 °2-0.0401725249368 °2--0.0250426661749 °2
S-0.00380507772941 Å °-0.0189392840257 Å °0.0086827464445 Å °0.00723299640856 Å °0.00392337188385 Å °-0.0106854018837 Å °-0.00863429490948 Å °0.0298059973549 Å °0.00343324400361 Å °
Refinement TLS groupSelection details: all

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