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- PDB-2vtu: crystal structure of bacteriophage MS2 covalent coat protein dimer -

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Basic information

Entry
Database: PDB / ID: 2vtu
Titlecrystal structure of bacteriophage MS2 covalent coat protein dimer
ComponentsMS2 COAT PROTEIN
KeywordsVIRUS / MS2 / DIMER / VIRION / OCTAHEDRON / RNA-BINDING / COAT PROTEIN / CAPSID PROTEIN
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
Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Biological speciesENTEROBACTERIO PHAGE MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPlevka, P. / Tars, K. / Liljas, L.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal Packing of a Bacteriophage MS2 Coat Protein Mutant Corresponds to Octahedral Particles.
Authors: Plevka, P. / Tars, K. / Liljas, L.
History
DepositionMay 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: MS2 COAT PROTEIN
L: MS2 COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,7442
Polymers54,7442
Non-polymers00
Water0
1
J: MS2 COAT PROTEIN
L: MS2 COAT PROTEIN
x 24


Theoretical massNumber of molelcules
Total (without water)1,313,85048
Polymers1,313,85048
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation23
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.438, 220.438, 220.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Number of models2
SymmetryPoint symmetry: (Schoenflies symbol: O (octahedral))
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein MS2 COAT PROTEIN


Mass: 27371.877 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-130,2 AND 4-130
Source method: isolated from a genetically manipulated source
Details: EACH CHAIN COMPRISES A REPEAT UNIT CONTAINING RESIDUES 2-130 (PDB RESIDUES 1-129), RESIDUE 2 (PDB RESIDUE 130) AND 4-130 (PDB RESIDUES 131-257)
Source: (gene. exp.) ENTEROBACTERIO PHAGE MS2 (virus) / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P03612

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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

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5
Details: 0.32M NA2HPO4, 0.08M NAH2PO4 AND 5% PEG 8000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: May 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.5→45 Å / Num. obs: 6079 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 17.3
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
BEASTphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 3.5→45 Å / Rfactor Rfree error: 0.083 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: THE DIFFRACTION DATA REPRESENTS AN AVERAGE OF TWO ORIENTATIONS DEMONSTRATED BY THE TWO MODELS. CHAIN J IN MODEL 1 AND 2 ARE APPROXIMATELY 180 DEGREES ROTATED TO EACH OTHER. THE SUBUNIT L HAS ...Details: THE DIFFRACTION DATA REPRESENTS AN AVERAGE OF TWO ORIENTATIONS DEMONSTRATED BY THE TWO MODELS. CHAIN J IN MODEL 1 AND 2 ARE APPROXIMATELY 180 DEGREES ROTATED TO EACH OTHER. THE SUBUNIT L HAS 0.25 OCCUPANCY, BECAUSE TWOFOLD CRYSTALLOGRAPHIC AXIS PUTS 180 DEGREE ROTATED COPY OF THE L SUBUNIT ON TOP OF ITSELF.
RfactorNum. reflection% reflectionSelection details
Rfree0.3102 308 5 %RANDOM
Rwork0.2723 ---
obs0.2723 6079 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.2947 Å2 / ksol: 0.984345 e/Å3
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.64 Å
Luzzati d res low-5 Å
Luzzati sigma a1.39 Å1.24 Å
Refinement stepCycle: LAST / Resolution: 3.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 0 0 3846
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.054
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.61
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.083 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.561 46 4.6 %
Rwork0.533 944 -
obs--99.4 %
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR_PROTEIN_REP.PARAM / Topol file: CNS_TOPPAR_PROTEIN.TOP

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