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- PDB-1bms: CRYSTAL STRUCTURE OF MS2 CAPSIDS WITH MUTATIONS IN THE SUBUNIT FG LOOP -

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Basic information

Entry
Database: PDB / ID: 1bms
TitleCRYSTAL STRUCTURE OF MS2 CAPSIDS WITH MUTATIONS IN THE SUBUNIT FG LOOP
ComponentsBACTERIOPHAGE MS2 CAPSID
KeywordsVIRUS / BACTERIOPHAGE COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacterio phage MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLiljas, L. / Stonehouse, N.J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structures of MS2 capsids with mutations in the subunit FG loop.
Authors: Stonehouse, N.J. / Valegard, K. / Golmohammadi, R. / van den Worm, S. / Walton, C. / Stockley, P.G. / Liljas, L.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure Determination of the Bacteriophage MS2
Authors: Valegard, K. / Liljas, L. / Fridborg, K. / Unge, T.
#2: Journal: Nature / Year: 1990
Title: The Three-Dimensional Structure of the Bacterial Virus MS2
Authors: Valegard, K. / Liljas, L. / Fridborg, K. / Unge, T.
#3: Journal: Semin.Virol. / Year: 1990
Title: The Structure of Bacteriophage MS2
Authors: Liljas, L. / Valegard, K.
#4: Journal: J.Mol.Biol. / Year: 1986
Title: Purification, Crystallization and Preliminary X-Ray Data of the Bacteriophage MS2
Authors: Valegard, K. / Unge, T. / Montelius, I. / Strandberg, B. / Fiers, W.
History
DepositionAug 29, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERIOPHAGE MS2 CAPSID
B: BACTERIOPHAGE MS2 CAPSID
C: BACTERIOPHAGE MS2 CAPSID


Theoretical massNumber of molelcules
Total (without water)41,2663
Polymers41,2663
Non-polymers00
Water3,099172
1
A: BACTERIOPHAGE MS2 CAPSID
B: BACTERIOPHAGE MS2 CAPSID
C: BACTERIOPHAGE MS2 CAPSID
x 60


Theoretical massNumber of molelcules
Total (without water)2,475,981180
Polymers2,475,981180
Non-polymers00
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BACTERIOPHAGE MS2 CAPSID
B: BACTERIOPHAGE MS2 CAPSID
C: BACTERIOPHAGE MS2 CAPSID
x 5


  • icosahedral pentamer
  • 206 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)206,33215
Polymers206,33215
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: BACTERIOPHAGE MS2 CAPSID
B: BACTERIOPHAGE MS2 CAPSID
C: BACTERIOPHAGE MS2 CAPSID
x 6


  • icosahedral 23 hexamer
  • 248 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)247,59818
Polymers247,59818
Non-polymers00
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: BACTERIOPHAGE MS2 CAPSID
B: BACTERIOPHAGE MS2 CAPSID
C: BACTERIOPHAGE MS2 CAPSID
x 10


  • crystal asymmetric unit, crystal frame
  • 413 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)412,66430
Polymers412,66430
Non-polymers00
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)288.000, 288.000, 653.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.75576191, -0.57734954), (0.75576185, 0.56366034, -0.33333315), (0.5773495, -0.33333315, 0.74535665)
3generate(-0.80901699, -0.46708655, -0.35682164), (0.46708651, -0.14235205, -0.87267752), (0.35682162, -0.87267752, 0.33333506)
4generate(-0.80901699, 0.46708655, 0.35682164), (-0.46708651, -0.14235205, -0.87267752), (-0.35682162, -0.87267752, 0.33333506)
5generate(0.30901699, 0.75576191, 0.57734954), (-0.75576185, 0.56366034, -0.33333315), (-0.5773495, -0.33333315, 0.74535665)
6generate(-1), (0.74535467, -0.66666814), (-0.66666814, -0.74535467)
7generate(-0.30901699, 0.75576191, 0.57734954), (0.17841012, 0.64234946, -0.74535695), (-0.9341725, -0.12732297, -0.33333247)
8generate(0.80901699, 0.46708655, 0.35682164), (0.11026351, 0.47568353, -0.87267813), (-0.57735035, 0.74535585, 0.33333345)
9generate(0.80901699, -0.46708655, -0.35682164), (-0.11026351, 0.47568353, -0.87267813), (0.57735035, 0.74535585, 0.33333345)
10generate(-0.30901699, -0.75576191, -0.57734954), (-0.17841012, 0.64234946, -0.74535695), (0.9341725, -0.12732297, -0.33333247)

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Components

#1: Protein BACTERIOPHAGE MS2 CAPSID


Mass: 13755.452 Da / Num. of mol.: 3 / Mutation: P78N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 %(w/v)MS21drop
20.2 Msodium phosphate1drop
31.5 %(w/v)PEG60001drop
40.02 %(w/v)1dropNaN3
50.4 Msodium phospahte1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87, 0.93, 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
20.931
30.951
ReflectionNum. obs: 140876 / Rmerge(I) obs: 0.09
Reflection
*PLUS
Highest resolution: 2.67 Å / Lowest resolution: 10.59 Å / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.67 Å / Lowest resolution: 2.74 Å / % possible obs: 7 % / Num. unique obs: 1468 / Rmerge(I) obs: 0.166

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.7→15 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.218 -
obs0.218 138822
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 0 172 3070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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