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- PDB-1mvb: STRUCTURE OF A PROTEIN CAPSID OF THE T59S MUTANT OF PHAGE MS2 -

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Basic information

Entry
Database: PDB / ID: 1mvb
TitleSTRUCTURE OF A PROTEIN CAPSID OF THE T59S MUTANT OF PHAGE MS2
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 / MIR / Resolution: 3 Å
AuthorsVandenworm, S. / Valegard, K. / Stonehouse, N.J. / Liljas, L.
CitationJournal: Nucleic Acids Res. / Year: 1998
Title: Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments.
Authors: van den Worm, S.H. / Stonehouse, N.J. / Valegard, K. / Murray, J.B. / Walton, C. / Fridborg, K. / Stockley, P.G. / Liljas, L.
History
DepositionAug 6, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: 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 / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / software / 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 / _software.name / _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 2.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine
Item: _refine.pdbx_method_to_determine_struct / _refine.pdbx_starting_model

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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)41,1733
Polymers41,1733
Non-polymers00
Water3,927218
1
A: BACTERIOPHAGE MS2 CAPSID
B: BACTERIOPHAGE MS2 CAPSID
C: BACTERIOPHAGE MS2 CAPSID
x 60


Theoretical massNumber of molelcules
Total (without water)2,470,399180
Polymers2,470,399180
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)205,86715
Polymers205,86715
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
  • 247 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)247,04018
Polymers247,04018
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
  • 412 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)411,73330
Polymers411,73330
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: 13724.438 Da / Num. of mol.: 3 / Mutation: T59S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: LevivirusEmesvirus / Species: Enterobacteria phage MS2Bacteriophage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal growpH: 7.4 / Details: 1.5 % PEG 6000, 0.2 M SODIUM PHOSPHATE PH 7.4
Crystal grow
*PLUS
Temperature: 37 ℃ / 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 phosphate1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 179377 / % possible obs: 89 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 7
Reflection shellResolution: 3→3.2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 3 / % possible all: 85
Reflection
*PLUS
Num. obs: 128511 / % possible obs: 61.8 % / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
Lowest resolution: 3.08 Å / % possible obs: 58.3 % / Redundancy: 2 % / Num. unique obs: 8748 / Rmerge(I) obs: 0.233

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 3→10 Å / σ(F): 2
Details: THE AXIAL SYSTEM OF THIS COORDINATE ENTRY HAS X,Y,Z COINCIDENT WITH THREE PERPENDICULAR TWO-FOLD AXIS IN THE ICOSAHEDRON. THE CRYSTAL X AND Y AXES ARE ALONG TWO-FOLD AXES OF THE ICOSAHEDRON, ...Details: THE AXIAL SYSTEM OF THIS COORDINATE ENTRY HAS X,Y,Z COINCIDENT WITH THREE PERPENDICULAR TWO-FOLD AXIS IN THE ICOSAHEDRON. THE CRYSTAL X AND Y AXES ARE ALONG TWO-FOLD AXES OF THE ICOSAHEDRON, AND THE Z AXIS ARE ALONG A THREE-FOLD AXIS.
RfactorNum. reflection% reflection
Rwork0.173 --
obs0.173 115167 62 %
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 218 3110
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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→3.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.235 4953
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.235

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