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- PDB-1fr5: PHAGE FR CAPSIDS WITH A FOUR RESIDUE DELETION IN THE COAT PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 1fr5
TitlePHAGE FR CAPSIDS WITH A FOUR RESIDUE DELETION IN THE COAT PROTEIN FG LOOP
ComponentsBACTERIOPHAGE FR CAPSID
KeywordsVIRUS / VIRAL COAT PROTEIN / CAPSID / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsAxblom, C. / Tars, K. / Fridborg, K. / Bundule, M. / Orna, L. / Liljas, L.
Citation
Journal: Virology / Year: 1998
Title: Structure of phage fr capsids with a deletion in the FG loop: implications for viral assembly.
Authors: Axblom, C. / Tars, K. / Fridborg, K. / Orna, L. / Bundule, M. / Liljas, L.
#1: 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.
History
DepositionJul 22, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: 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_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper / struct_ref_seq_dif
Item: _atom_site.Cartn_y / _atom_site.Cartn_z ..._atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2May 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)40,0023
Polymers40,0023
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)2,400,117180
Polymers2,400,117180
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
  • 200 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)200,01015
Polymers200,01015
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
  • 240 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)240,01218
Polymers240,01218
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 10


  • crystal asymmetric unit, crystal frame
  • 400 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)400,01930
Polymers400,01930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)264.100, 264.100, 654.200
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, -0.75576189, 0.57734953), (0.75576187, 0.56366035, 0.33333315), (-0.57734952, 0.33333315, 0.74535664)
3generate(-0.80901699, -0.46708653, 0.35682164), (0.46708652, -0.14235203, 0.87267753), (-0.35682163, 0.87267753, 0.33333504)
4generate(-0.80901699, 0.46708653, -0.35682164), (-0.46708652, -0.14235203, 0.87267753), (0.35682163, 0.87267753, 0.33333504)
5generate(0.30901699, 0.75576189, -0.57734953), (-0.75576187, 0.56366035, 0.33333315), (0.57734952, 0.33333315, 0.74535664)
6generate(-1), (0.74535469, 0.66666813), (0.66666813, -0.74535469)
7generate(-0.30901699, 0.75576189, -0.57734953), (0.17841013, 0.64234947, 0.74535694), (0.93417252, 0.12732296, -0.33333248)
8generate(0.80901699, 0.46708653, -0.35682164), (0.11026352, 0.47568353, 0.87267813), (0.57735037, -0.74535585, 0.33333345)
9generate(0.80901699, -0.46708653, 0.35682164), (-0.11026352, 0.47568353, 0.87267813), (-0.57735037, -0.74535585, 0.33333345)
10generate(-0.30901699, -0.75576189, 0.57734953), (-0.17841013, 0.64234947, 0.74535694), (-0.93417252, 0.12732296, -0.33333248)

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Components

#1: Protein BACTERIOPHAGE FR CAPSID


Mass: 13333.982 Da / Num. of mol.: 3 / Mutation: DEL(70-73)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage fr (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Plasmid: PFRS5 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P03614

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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

Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %satammonium sulfate1drop
250 mMMops1drop
30.02 %(w/v)1dropNaN3
430 %satammonium sulfate1reservoir
550 mMMops1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 52800 / % possible obs: 48 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.9
Reflection shellResolution: 3.5→3.56 Å / Rmerge(I) obs: 0.387 / % possible all: 26
Reflection shell
*PLUS
% possible obs: 26 % / Num. unique obs: 1419

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FRS

1frs


Resolution: 3.5→30 Å / Isotropic thermal model: RESTRAINED
RfactorNum. reflection% reflection
Rwork0.256 --
obs0.256 51856 47.8 %
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 0 0 2752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
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
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3.5→3.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.351 1320 -
obs--26 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.351

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