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- PDB-1qbe: BACTERIOPHAGE Q BETA CAPSID -

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Basic information

Entry
Database: PDB / ID: 1qbe
TitleBACTERIOPHAGE Q BETA CAPSID
ComponentsBACTERIOPHAGE Q BETA CAPSID
KeywordsVIRUS / COAT PROTEIN / RNA BINDING / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / translation repressor activity / 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 Qbeta (virus)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsLiljas, L. / Golmohammadi, R.
Citation
Journal: Structure / Year: 1996
Title: The crystal structure of bacteriophage Q beta at 3.5 A resolution.
Authors: Golmohammadi, R. / Fridborg, K. / Bundule, M. / Valegard, K. / Liljas, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Bacteriophage Qb
Authors: Valegard, K. / Fridborg, K. / Liljas, L.
History
DepositionJan 10, 1996Processing site: BNL
Revision 1.0Jul 11, 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 / struct_ncs_oper
Item: _atom_site.Cartn_x / _cell.Z_PDB ..._atom_site.Cartn_x / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx_vector[1] / _pdbx_database_status.process_site / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _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]
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 Q BETA CAPSID
B: BACTERIOPHAGE Q BETA CAPSID
C: BACTERIOPHAGE Q BETA CAPSID


Theoretical massNumber of molelcules
Total (without water)42,4113
Polymers42,4113
Non-polymers00
Water00
1
A: BACTERIOPHAGE Q BETA CAPSID
B: BACTERIOPHAGE Q BETA CAPSID
C: BACTERIOPHAGE Q BETA CAPSID
x 60


Theoretical massNumber of molelcules
Total (without water)2,544,637180
Polymers2,544,637180
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 Q BETA CAPSID
B: BACTERIOPHAGE Q BETA CAPSID
C: BACTERIOPHAGE Q BETA CAPSID
x 5


  • icosahedral pentamer
  • 212 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)212,05315
Polymers212,05315
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: BACTERIOPHAGE Q BETA CAPSID
B: BACTERIOPHAGE Q BETA CAPSID
C: BACTERIOPHAGE Q BETA CAPSID
x 6


  • icosahedral 23 hexamer
  • 254 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)254,46418
Polymers254,46418
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 Q BETA CAPSID
B: BACTERIOPHAGE Q BETA CAPSID
C: BACTERIOPHAGE Q BETA CAPSID
x 30


  • crystal asymmetric unit, crystal frame
  • 1.27 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)1,272,31990
Polymers1,272,31990
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)477.800, 295.200, 477.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5)51.05465, -36.94349, 59.77583
3generate(-0.80901699, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699), (-0.5, 0.80901699, -0.30901699)133.66282, -22.83234, 36.94349
4generate(-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699), (0.5, 0.80901699, -0.30901699)133.66282, 22.83234, -36.94349
5generate(0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699), (0.80901699, 0.30901699, 0.5)51.05465, 36.94349, -59.77583
6generate(-1), (1), (-1)147.77398
7generate(-0.30901699, 0.5, -0.80901699), (0.5, 0.80901699, 0.30901699), (0.80901699, -0.30901699, -0.5)96.71933, -36.94349, -59.77583
8generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)14.11116, -22.83234, -36.94349
9generate(0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699)14.11116, 22.83234, 36.94349
10generate(-0.30901699, -0.5, 0.80901699), (-0.5, 0.80901699, 0.30901699), (-0.80901699, -0.30901699, -0.5)96.71933, 36.94349, 59.77583
11generate(-1), (1), (-1)73.88699, 73.88699
12generate(-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5), (-0.30901699, 0.5, -0.80901699)110.83048, 59.77583, 22.83234
13generate(-0.30901699, -0.5, -0.80901699), (-0.5, 0.80901699, -0.30901699), (0.80901699, 0.30901699, -0.5)96.71933, 36.94349, -59.77583
14generate(0.30901699, -0.5, -0.80901699), (0.5, 0.80901699, -0.30901699), (0.80901699, -0.30901699, 0.5)51.05465, -36.94349, -59.77583
15generate(0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699)36.94349, -59.77583, 22.83234
16generate(1), (1), (1)73.88699, -73.88699
17generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)36.94349, 59.77583, -22.83234
18generate(0.30901699, 0.5, 0.80901699), (-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5)51.05465, 36.94349, 59.77583
19generate(-0.30901699, 0.5, 0.80901699), (0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5)96.71933, -36.94349, 59.77583
20generate(-0.5, 0.80901699, 0.30901699), (0.80901699, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699)110.83048, -59.77583, -22.83234
21generate(-1), (-1), (1)73.88699, 73.88699
22generate(0.80901699, -0.30901699, -0.5), (-0.30901699, 0.5, -0.80901699), (0.5, 0.80901699, 0.30901699)14.11116, 22.83234, -36.94349
23generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)36.94349, -59.77583, -22.83234
24generate(-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699)110.83048, -59.77583, 22.83234
25generate(-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.5, 0.80901699), (-0.5, 0.80901699, 0.30901699)133.66282, 22.83234, 36.94349
26generate(1), (1), (1)73.88699, -73.88699
27generate(-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.30901699)133.66282, -22.83234, -36.94349
28generate(-0.5, 0.80901699, -0.30901699), (-0.80901699, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699)110.83048, 59.77583, -22.83234
29generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.30901699, -0.5), (-0.30901699, 0.5, 0.80901699)36.94349, 59.77583, 22.83234
30generate(0.80901699, 0.30901699, 0.5), (0.30901699, 0.5, -0.80901699), (-0.5, 0.80901699, 0.30901699)14.11116, -22.83234, 36.94349

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Components

#1: Protein BACTERIOPHAGE Q BETA CAPSID


Mass: 14136.874 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage Qbeta (virus) / Genus: Allolevivirus / Species: Enterobacteria phage Qbeta sensu lato / References: UniProt: P03615

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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: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG20001drop
20.3-0.45 Mammonium sulfate1drop
30-0.2 Mlithium chloride1drop
45 mg/mlHEPES1drop
50.4 Msodium chloride1reservoir
650 mMTris1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 328697
Reflection
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 40 Å / Num. obs: 333576 / % possible obs: 80.5 % / Num. measured all: 800000 / Rmerge(I) obs: 0.201

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 3.5→15 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.304 -
obs0.304 328697
Displacement parametersBiso mean: 32.6 Å2
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 0 0 2808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
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
Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.344 / Rfactor Rwork: 0.344
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1

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