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- PDB-7m54: Crystallographic structure of a cubic crystal form of STMV grown ... -

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Basic information

Entry
Database: PDB / ID: 7m54
TitleCrystallographic structure of a cubic crystal form of STMV grown from bromide
ComponentsCoat protein
KeywordsVIRUS
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: 3.8 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 22, 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 1.2Aug 16, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Oct 18, 2023Group: Refinement description / Category: 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)365,787220
Polymers350,67920
Non-polymers15,108200
Water10,449580
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)1,097,361660
Polymers1,052,03760
Non-polymers45,324600
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)234.650, 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
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
11D-213-

BR

21D-214-

BR

31L-210-

BR

41M-201-

BR

51M-205-

BR

61KK-202-

BR

71KK-218-

BR

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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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Non-polymers , 5 types, 780 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 182 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 3.07 Å3/Da / Density % sol: 59.92 % / 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 6 to 8 ul and composed of equal volumes of a 5 mg/ml virus stock solution buffered ...Details: crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. Drops were 6 to 8 ul and composed of equal volumes of a 5 mg/ml virus stock solution buffered at pH 6.5 with 0.1M phosphate, and the reservoir solution. The reservoir solution was 18% w/v NaBr 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 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→105 Å / Num. obs: 38017 / % possible obs: 73 % / Redundancy: 4.6 % / Biso Wilson estimate: 50.24 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.21 / Rsym value: 0.2 / Net I/σ(I): 7.7
Reflection shellResolution: 3.5→3.65 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1200 / CC1/2: 0.32 / Rsym value: 0.3

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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: 3.8→56.91 Å / SU ML: 0.5762 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.6351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2853 1305 4.95 %
Rwork0.2131 31911 -
obs0.2188 33573 78.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.34 Å2
Refinement stepCycle: LAST / Resolution: 3.8→56.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23322 0 200 580 24102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005324203
X-RAY DIFFRACTIONf_angle_d0.64933068
X-RAY DIFFRACTIONf_chiral_restr0.04853851
X-RAY DIFFRACTIONf_plane_restr0.00694325
X-RAY DIFFRACTIONf_dihedral_angle_d10.64118946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.910.3885790.22081610X-RAY DIFFRACTION47.86
3.91-4.040.42611100.2391664X-RAY DIFFRACTION50.38
4.04-4.180.3218980.20631860X-RAY DIFFRACTION56.01
4.18-4.350.39111040.21052105X-RAY DIFFRACTION63.17
4.35-4.550.35271240.18182362X-RAY DIFFRACTION70.17
4.55-4.790.28471360.18752645X-RAY DIFFRACTION78.6
4.79-5.090.341660.18122910X-RAY DIFFRACTION87.11
5.09-5.480.30021710.19483175X-RAY DIFFRACTION94.65
5.48-6.030.30341770.21543328X-RAY DIFFRACTION98.79
6.03-6.90.31691660.22893391X-RAY DIFFRACTION99.39
6.9-8.680.28871730.23273403X-RAY DIFFRACTION99.83
8.69-56.910.32991580.24183458X-RAY DIFFRACTION97.15
Refinement TLS params.Method: refined / Origin x: 88.363990023 Å / Origin y: 174.697357596 Å / Origin z: 27.1460215295 Å
111213212223313233
T0.304652385625 Å20.0256917462944 Å2-0.00940164958434 Å2-0.360154897962 Å2-0.0150136492587 Å2--0.40303454819 Å2
L0.056638795757 °2-0.0291262011398 °20.0940650885899 °2--0.0651092423384 °2-0.0423509949614 °2--0.0927307797225 °2
S0.0266369794533 Å °0.0388396660357 Å °-0.0371385964133 Å °-0.00824453020805 Å °-0.0117463753218 Å °-0.051270349264 Å °0.0717888277473 Å °0.100170205433 Å °0.076636088968 Å °
Refinement TLS groupSelection details: all

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