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- PDB-1gff: THE ATOMIC STRUCTURE OF THE DEGRADED PROCAPSID PARTICLE OF THE BA... -

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Entry
Database: PDB / ID: 1gff
TitleTHE ATOMIC STRUCTURE OF THE DEGRADED PROCAPSID PARTICLE OF THE BACTERIOPHAGE G4: INDUCED STRUCTURAL CHANGES IN THE PRESENCE OF CALCIUM IONS AND FUNCTIONAL IMPLICATIONS
Components(BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ) x 3
KeywordsVIRUS / COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


modulation by virus of host process / T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Microvirus J protein-like / Microvirus J protein / Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus ...Microvirus J protein-like / Microvirus J protein / Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Capsid protein F / Major spike protein G / DNA-binding protein J
Similarity search - Component
Biological speciesEnterobacteria phage G4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsRossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Atomic structure of the degraded procapsid particle of the bacteriophage G4: induced structural changes in the presence of calcium ions and functional implications.
Authors: McKenna, R. / Bowman, B.R. / Ilag, L.L. / Rossmann, M.G. / Fane, B.A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Analysis of the Single-Stranded DNA Bacteriophage PhiX174 Refined at a Resolution of 3.0 Angstroms
Authors: McKenna, R. / Ilag, L.L. / Rossmann, M.G.
#2: Journal: Nature / Year: 1992
Title: Atomic Structure of Single-Stranded DNA Bacteriophage PhiX174 and its Functional Implications
Authors: McKenna, R. / Xia, D. / Willingmann, P. / Ilag, L.L. / Krishnaswamy, S. / Rossmann, M.G. / Olson, N.H. / Baker, T.S. / Incardona, N.L.
#3: Journal: The Bacteriophages (The Viruses) / Year: 1988
Title: Biology of the Bacteriophage PhiX174
Authors: Hayashi, M. / Aoyama, A. / Delwood, L. / Richardson, D.L. / Hayashi, M.N.
#4: Journal: The Single-Stranded DNA Phages / Year: 1978
Title: Comparative DNA Sequence Analysis of the G4 and PhiX174 Genomes
Authors: Godson, G.N. / Fiddles, J.C. / Barrell, B.G. / Sanger, F.
History
DepositionNov 6, 1995Processing 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_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_ncs_oper / struct_ref_seq_dif
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_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[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_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_close_contact.dist / _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 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET STRAND 4 OF SHEET G2 IS BIFURCATED. SHEET G2 IS REPRESENTED BY TWO SHEETS G2A AND G2B WHICH ...SHEET STRAND 4 OF SHEET G2 IS BIFURCATED. SHEET G2 IS REPRESENTED BY TWO SHEETS G2A AND G2B WHICH DIFFER ONLY IN STRAND 4.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
2: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
3: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ


Theoretical massNumber of molelcules
Total (without water)70,2713
Polymers70,2713
Non-polymers00
Water00
1
1: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
2: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
3: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
x 60


Theoretical massNumber of molelcules
Total (without water)4,216,280180
Polymers4,216,280180
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
1: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
2: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
3: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
x 5


  • icosahedral pentamer
  • 351 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)351,35715
Polymers351,35715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
2: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
3: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
x 6


  • icosahedral 23 hexamer
  • 422 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)421,62818
Polymers421,62818
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
1: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
2: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
3: BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ
x 20


  • crystal asymmetric unit, crystal frame
  • 1.41 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,405,42760
Polymers1,405,42760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)414.200, 414.200, 263.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.56366104, -0.75576134, 0.33333331), (0.75576129, 0.30901696, -0.57735029), (0.33333333, 0.57735025, 0.74535598)158.81495, 203.20142, -121.32382
3generate(-0.14235028, -0.46708622, 0.87267801), (0.46708616, -0.80901701, -0.35682211), (0.87267798, 0.35682204, 0.33333331)54.31971, 456.06663, -41.49655
4generate(-0.14235032, 0.46708615, 0.87267806), (-0.46708617, -0.80901697, 0.35682209), (0.87267796, -0.35682214, 0.33333331)-169.07685, 409.14452, 129.16324
5generate(0.56366098, 0.75576131, 0.33333338), (-0.75576128, 0.30901703, 0.57735029), (0.33333332, -0.5773503, 0.74535598)-202.64828, 127.27984, 154.80952
6generate(0.64235036, -0.75576135, 0.12732195), (-0.17841105, -0.30901699, -0.93417237), (0.74535594, 0.57735026, -0.33333336)172.3602, 374.45817, -50.4
7generate(-0.16666664, -0.64549727, 0.74535599), (-0.64549723, -0.49999997, -0.57735025), (0.74535596, -0.57735027, -0.33333339)105.35608, 396.66849, 225.73334
8generate(-0.33333335, 0.35682206, 0.87267804), (-0.93417235, -0.35682207), (-0.12732199, -0.93417236, 0.33333328)-142.70847, 262.59952, 267.22989
9generate(0.37267796, 0.86602541, 0.33333337), (-0.6454972, 0.50000005, -0.57735026), (-0.66666665, 0.74535598)-229.01667, 157.53001, 16.74285
10generate(0.97568365, 0.17841105, -0.12732204), (-0.17841104, 0.30901701, -0.93417237), (-0.12732203, 0.93417235, 0.33333334)-34.29352, 226.66246, -179.56322

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Components

#1: Protein BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ


Mass: 48611.625 Da / Num. of mol.: 1 / Mutation: AM(E)W4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage G4 (virus) / Genus: Microvirus / Species: Enterobacteria phage G4 sensu lato / Species (production host): Escherichia coli / Production host: Escherichia coli C (bacteria) / Strain (production host): C / References: UniProt: P03642
#2: Protein BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ


Mass: 18837.395 Da / Num. of mol.: 1 / Mutation: AM(E)W4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage G4 (virus) / Genus: Microvirus / Species: Enterobacteria phage G4 sensu lato / Species (production host): Escherichia coli / Production host: Escherichia coli C (bacteria) / Strain (production host): C / References: UniProt: P03644
#3: Protein/peptide BACTERIOPHAGE G4 CAPSID PROTEINS GPF, GPG, GPJ


Mass: 2822.318 Da / Num. of mol.: 1 / Mutation: AM(E)W4 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage G4 (virus) / Genus: Microvirus / Species: Enterobacteria phage G4 sensu lato / References: UniProt: P03652

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.125 mg/mlvirus1drop
31.5-2.0 %(w/v)PEG80001reservoir
490-93 mMbis-Tris-methane1reservoir
2reservoir solution1drop0.005ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementResolution: 3→6 Å / Rfactor Rwork: 0.352 / σ(F): 3
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4779 0 0 0 4779
Refinement
*PLUS
Rfactor obs: 0.352
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_bond_d / Dev ideal: 0.031

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