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- PDB-1yc6: Crystallographic Structure of the T=1 Particle of Brome Mosaic Virus -

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Basic information

Entry
Database: PDB / ID: 1yc6
TitleCrystallographic Structure of the T=1 Particle of Brome Mosaic Virus
ComponentsCoat protein
KeywordsVIRUS / Structural Transition / Proteolysis / BMV / AlMV / Symmetry / Assembly / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell endoplasmic reticulum / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Satellite virus coat domain / Bromovirus coat protein / Bromovirus coat protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBrome mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLarson, S.B. / Lucas, R.W. / McPherson, A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystallographic structure of the T=1 particle of brome mosaic virus.
Authors: Larson, S.B. / Lucas, R.W. / McPherson, A.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: THE CRYSTALLOGRAPHIC STRUCTURE OF BROME MOSAIC VIRUS
Authors: Lucas, R.W. / Larson, S.B. / McPherson, A.
#2: Journal: VIROLOGY / Year: 2001
Title: CRYSTALLIZATION OF BROME MOSAIC VIRUS AND T=1 BROME MOSAIC VIRUS PARTICLES FOLLOWING A STRUCTURAL TRANSITION
Authors: Lucas, R.W. / Kuznetsov, Y.G. / Larson, S.B. / McPherson, A.
History
DepositionDec 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Coat protein
Q: Coat protein
R: Coat protein
S: Coat protein
T: Coat protein
U: Coat protein
V: Coat protein
W: Coat protein
X: Coat protein
Y: Coat protein
Z: Coat protein
1: Coat protein
2: Coat protein
3: Coat protein
4: Coat protein


Theoretical massNumber of molelcules
Total (without water)494,03730
Polymers494,03730
Non-polymers00
Water8,107450
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: Coat protein
Q: Coat protein
R: Coat protein
S: Coat protein
T: Coat protein
U: Coat protein
V: Coat protein
W: Coat protein
X: Coat protein
Y: Coat protein
Z: Coat protein
1: Coat protein
2: Coat protein
3: Coat protein
4: Coat protein

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: Coat protein
Q: Coat protein
R: Coat protein
S: Coat protein
T: Coat protein
U: Coat protein
V: Coat protein
W: Coat protein
X: Coat protein
Y: Coat protein
Z: Coat protein
1: Coat protein
2: Coat protein
3: Coat protein
4: Coat protein


Theoretical massNumber of molelcules
Total (without water)988,07460
Polymers988,07460
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area220070 Å2
ΔGint-1075 kcal/mol
Surface area361300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)194.770, 194.770, 428.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3
DetailsThe biological unit is a T=1 quasi-icosahedral particle generated by the twofold operation -x, y, -z

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Components

#1: Protein ...
Coat protein / Capsid protein / CP


Mass: 16467.896 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Brome mosaic virus / Genus: Bromovirus / References: UniProt: P03602
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 4.12 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium malonate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.1 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jul 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→30.3 Å / Num. all: 181726 / Num. obs: 181726 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.9 % / Biso Wilson estimate: 62.6 Å2 / Rsym value: 0.153 / Net I/σ(I): 8.07
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 1.93 / Num. unique all: 17389 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
SDMSdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JS9

1js9


Resolution: 2.9→30.26 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 173427.88 / Data cutoff high rms absF: 173427.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 7904 5 %RANDOM
Rwork0.219 ---
all0.234 181726 --
obs0.22 157521 86.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.5033 Å2 / ksol: 0.300427 e/Å3
Displacement parametersBiso mean: 62.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.9→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34800 0 0 450 35250
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.942.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight Biso Weight position
11RESTRAINTX-RAY DIFFRACTION0.0582120
22X-RAY DIFFRACTION0.17110120
33X-RAY DIFFRACTION0.24910120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.9-30.3666015.30.353106870.0151127162.7
3-3.120.3356140.3240.0141214467.7
3.12-3.270.3286640.2960.0131389076.9
3.27-3.440.2977460.2730.0111535385
3.44-3.650.2698230.2530.0091593988.3
3.65-3.930.2448360.2230.0081694493.5
3.93-4.330.2328450.20.0081735895.3
4.33-4.950.2039520.1850.0071782997.7
4.95-6.230.2029180.1750.0071811698.4
6.23-30.260.2159060.2030.0071867698.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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