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- PDB-1frs: CRYSTAL STRUCTURE OF BACTERIOPHAGE FR CAPSIDS AT 3.5 ANGSTROMS RE... -

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Entry
Database: PDB / ID: 1frs
TitleCRYSTAL STRUCTURE OF BACTERIOPHAGE FR CAPSIDS AT 3.5 ANGSTROMS RESOLUTION
ComponentsBACTERIOPHAGE FR CAPSID
KeywordsVIRUS / COAT PROTEIN (VIRAL) / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA 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 speciesEnterobacteria phage fr (virus)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsLiljas, L. / Valegard, K. / Bundule, M.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of bacteriophage fr capsids at 3.5 A resolution.
Authors: Liljas, L. / Fridborg, K. / Valegard, K. / Bundule, M. / Pumpens, P.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of Bacteriophage Fr and its Recombinant Capsids
Authors: Bundule, M. / Pumpens, P. / Ose, V. / Valegard, K. / Liljas, L.
History
DepositionAug 16, 1994Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_database_status.process_site / _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_peptide_omega.omega / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,2393
Polymers41,2393
Non-polymers00
Water00
1
A: BACTERIOPHAGE FR CAPSID
B: BACTERIOPHAGE FR CAPSID
C: BACTERIOPHAGE FR CAPSID
x 60


Theoretical massNumber of molelcules
Total (without water)2,474,356180
Polymers2,474,356180
Non-polymers00
Water0
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 FR CAPSID
B: BACTERIOPHAGE FR CAPSID
C: BACTERIOPHAGE FR CAPSID
x 5


  • icosahedral pentamer
  • 206 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)206,19615
Polymers206,19615
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: BACTERIOPHAGE FR CAPSID
B: BACTERIOPHAGE FR CAPSID
C: BACTERIOPHAGE FR CAPSID
x 6


  • icosahedral 23 hexamer
  • 247 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)247,43618
Polymers247,43618
Non-polymers00
Water0
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 FR CAPSID
B: BACTERIOPHAGE FR CAPSID
C: BACTERIOPHAGE FR CAPSID
x 30


  • crystal asymmetric unit, crystal frame
  • 1.24 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)1,237,17890
Polymers1,237,17890
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)422.900, 305.900, 274.800
Angle α, β, γ (deg.)90.00, 129.80, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO B 78
2: ASN C 116 - PRO C 117 OMEGA = 212.01 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.37294718, -0.58660434, 0.71889201), (0.22902866, 0.80901699, 0.54132926), (-0.89914196, -0.03724036, 0.43606981)
3generate(-0.64164558, -0.72011711, 0.26404976), (-0.2160282, 0.5, 0.8386488), (-0.73595024, 0.48107311, -0.47638839)
4generate(-0.64164558, -0.2160282, -0.73595024), (-0.72011711, 0.5, 0.48107311), (0.26404976, 0.8386488, -0.47638839)
5generate(0.37294718, 0.22902866, -0.89914196), (-0.58660434, 0.80901699, -0.03724036), (0.71889201, 0.54132926, 0.43606981)
6generate(-0.33051439, -0.94380095), (-1), (-0.94380095, 0.33051439)
7generate(0.72534663, 0.22902866, -0.64916726), (-0.22902866, -0.80901699, -0.54132926), (-0.64916726, 0.54132926, -0.53436362)
8generate(0.90666363, -0.2160282, 0.36234357), (0.2160282, -0.5, -0.8386488), (0.36234357, 0.8386488, -0.40666363)
9generate(-0.03713732, -0.72011711, 0.69285796), (0.72011711, -0.5, -0.48107311), (0.69285796, 0.48107311, 0.53713732)
10generate(-0.80175538, -0.58660434, -0.11438375), (0.58660434, -0.80901699, 0.03724036), (-0.11438375, -0.03724036, 0.99273838)
11generate(0.47190047, -0.815633, 0.33474281), (-0.57856962, 0.815633), (-0.66525719, -0.57856962, -0.47190047)
12generate(-0.31179068, -0.94914576, 0.0436907), (-0.94914576, 0.30901699, -0.06025615), (0.0436907, -0.06025615, -0.9972263)
13generate(-0.37294718, -0.58660434, -0.71889201), (-0.22902866, 0.80901699, -0.54132926), (0.89914196, -0.03724036, -0.43606981)
14generate(0.37294718, -0.22902866, -0.89914196), (0.58660434, 0.80901699, 0.03724036), (0.71889201, -0.54132926, 0.43606981)
15generate(0.89509174, -0.37057614, -0.24795982), (0.37057614, 0.30901699, 0.87588915), (-0.24795982, -0.87588915, 0.41392524)
16generate(-0.47190047, -0.815633, -0.33474281), (0.57856962, -0.815633), (0.66525719, -0.57856962, 0.47190047)
17generate(-0.06181598, -0.37057614, -0.92674273), (0.94914576, -0.30901699, 0.06025615), (-0.30870875, -0.87588915, 0.37083297)
18generate(0.72534663, -0.22902866, -0.64916726), (0.22902866, -0.80901699, 0.54132926), (-0.64916726, -0.54132926, -0.53436362)
19generate(0.80175538, -0.58660434, 0.11438375), (-0.58660434, -0.80901699, -0.03724036), (0.11438375, -0.03724036, -0.99273838)
20generate(0.06181598, -0.94914576, 0.30870875), (-0.37057614, -0.30901699, -0.87588915), (0.92674273, -0.06025615, -0.37083297)
21generate(0.47190047, -0.57856962, -0.66525719), (-0.815633, -0.57856962), (0.33474281, 0.815633, -0.47190047)
22generate(0.64164558, -0.72011711, -0.26404976), (0.2160282, 0.5, -0.8386488), (0.73595024, 0.48107311, 0.47638839)
23generate(0.31179068, -0.94914576, -0.0436907), (0.94914576, 0.30901699, 0.06025615), (-0.0436907, -0.06025615, 0.9972263)
24generate(-0.06181598, -0.94914576, -0.30870875), (0.37057614, -0.30901699, 0.87588915), (-0.92674273, -0.06025615, 0.37083297)
25generate(0.03713732, -0.72011711, -0.69285796), (-0.72011711, -0.5, 0.48107311), (-0.69285796, 0.48107311, -0.53713732)
26generate(-0.47190047, -0.57856962, 0.66525719), (0.815633, 0.57856962), (-0.33474281, 0.815633, 0.47190047)
27generate(-0.90666363, -0.2160282, -0.36234357), (-0.2160282, -0.5, 0.8386488), (-0.36234357, 0.8386488, 0.40666363)
28generate(-0.06181598, 0.37057614, -0.92674273), (-0.94914576, -0.30901699, -0.06025615), (-0.30870875, 0.87588915, 0.37083297)
29generate(0.89509174, 0.37057614, -0.24795982), (-0.37057614, 0.30901699, -0.87588915), (-0.24795982, 0.87588915, 0.41392524)
30generate(0.64164558, -0.2160282, 0.73595024), (0.72011711, 0.5, -0.48107311), (-0.26404976, 0.8386488, 0.47638839)

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Components

#1: Protein BACTERIOPHAGE FR CAPSID


Mass: 13746.423 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage fr (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03614

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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: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125-28 mg/mlprotein1drop
210 %satammonium sulfate1drop
350 mMMOPS1drop
40.02 %(w/v)1dropNaN3
530 %satammonium sulfate1reservoir
650 mMMOPS1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 130705 / % possible obs: 38 %
Reflection
*PLUS
Highest resolution: 3.47 Å / Lowest resolution: 9.35 Å / Rmerge(I) obs: 0.137
Reflection shell
*PLUS
Highest resolution: 3.47 Å / Lowest resolution: 3.68 Å / % possible obs: 16 % / Num. unique obs: 8708 / Rmerge(I) obs: 0.283

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→20 Å / σ(F): 2
RfactorNum. reflection
Rfree0.236 -
Rwork0.228 -
obs0.228 129951
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 0 0 2898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.029
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_deg4.1
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.5

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