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- PDB-2wbh: Icosahedral particle of covalent coat protein dimer of bacterioph... -

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Basic information

Entry
Database: PDB / ID: 2wbh
TitleIcosahedral particle of covalent coat protein dimer of bacteriophage MS2
ComponentsCOAT PROTEIN
KeywordsVIRUS / CAPSID PROTEIN / COVALENT DIMER / VIRION / RNA-BINDING
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 speciesENTEROBACTERIA PHAGE MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.7 Å
AuthorsPlevka, P. / Tars, K. / Liljas, L.
CitationJournal: Protein Sci. / Year: 2009
Title: Structure and Stability of Icosahedral Particles of a Covalent Coat Protein Dimer of Bacteriophage MS2.
Authors: Plevka, P. / Tars, K. / Liljas, L.
History
DepositionFeb 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Refinement description / Version format compliance
Revision 1.2Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)82,1163
Polymers82,1163
Non-polymers00
Water00
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)4,926,938180
Polymers4,926,938180
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: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 5


  • icosahedral pentamer
  • 411 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)410,57815
Polymers410,57815
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 6


  • icosahedral 23 hexamer
  • 493 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)492,69418
Polymers492,69418
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
Unit cell
Length a, b, c (Å)368.200, 368.200, 368.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.485628, -0.246072, 0.838817), (0.730527, 0.641239, -0.234823), (-0.480099, 0.726815, 0.491167)80.33688, -159.59705, 136.43258
3generate(-0.346643, 0.332374, 0.877135), (0.935946, 0.060752, 0.346864), (0.062001, 0.941189, -0.332143)273.06512, -235.28614, 48.87647
4generate(-0.346643, 0.935946, 0.062001), (0.332374, 0.060752, 0.941189), (0.877135, 0.346864, -0.332143)311.84083, -122.46751, -141.66876
5generate(0.485628, 0.730527, -0.480099), (-0.246072, 0.641239, 0.726815), (0.838817, -0.234823, 0.491167)143.07731, 22.94732, -171.87608
6generate(-0.94101, 0.332714, 0.061661), (0.332714, 0.876557, 0.347777), (0.061661, 0.347777, -0.935547)641.80477, -163.70689, 269.33371
7generate(-0.243528, 0.489722, -0.837178), (0.634957, 0.732981, 0.244067), (0.73316, -0.472135, -0.489453)521.51941, -229.42551, 91.14398
8generate(0.641419, -0.234519, -0.730467), (0.72664, 0.491162, 0.480369), (0.246122, -0.838904, 0.485452)309.57866, -262.09805, 158.61772
9generate(0.490865, -0.839133, 0.234323), (0.48106, 0.485286, 0.730123), (-0.726384, -0.245668, 0.641883)298.87743, -216.57217, 378.50851
10generate(-0.48713, -0.488564, 0.723885), (0.2376, 0.723473, 0.648176), (-0.840387, 0.487741, -0.236343)504.20446, -155.76309, 446.93475
11generate(-0.064958, -0.339675, 0.938297), (-0.339675, -0.876605, -0.340858), (0.938297, -0.340858, -0.058436)281.93685, 533.44823, -87.8439
12generate(-0.730163, 0.48014, 0.486135), (-0.641695, -0.72627, -0.246496), (0.234713, -0.491933, 0.838399)458.94369, 599.55937, 33.96323
13generate(-0.237225, 0.840888, -0.486447), (-0.723843, -0.486966, -0.48879), (-0.647901, 0.236158, 0.724191)389.98042, 630.28803, 245.7152
14generate(0.732632, 0.244028, -0.635375), (-0.472593, -0.489404, -0.732898), (-0.489803, 0.837218, -0.243227)170.35193, 583.16826, 254.77799
15generate(0.839098, -0.4856, 0.245166), (-0.235164, -0.730215, -0.64147), (0.490522, 0.480603, -0.726918)103.57733, 523.31798, 48.62713
16generate(0.005968, 0.006961, -0.999958), (0.006961, -0.999952, -0.00692), (-0.999958, -0.00692, -0.006016)548.56837, 367.14512, 554.42152
17generate(0.488063, -0.723789, -0.487774), (-0.723789, -0.647951, 0.237252), (-0.487774, 0.237252, -0.840112)411.50999, 526.34966, 474.37154
18generate(-0.057551, -0.938743, 0.339779), (-0.938743, -0.064948, -0.338443), (0.339779, -0.338443, -0.8775)499.68578, 603.98262, 282.70194
19generate(-0.876853, -0.34084, 0.339051), (-0.34084, -0.056634, -0.938414), (0.339051, -0.938414, -0.066512)691.23979, 492.75789, 244.29359
20generate(-0.837596, 0.243637, -0.488952), (0.243637, -0.634498, -0.733521), (-0.488952, -0.733521, 0.472094)721.45089, 346.38427, 412.22552

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Components

#1: Protein COAT PROTEIN / ICOSAHEDRAL PARTICLE OF BACTERIOPHAGE MS2 COVALENT COAT PROTEIN DIMER


Mass: 27371.877 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-130,2 AND 4-130
Source method: isolated from a genetically manipulated source
Details: COVALENT DIMER OF MS2 COAT PROTEIN SUBUNITS, SERINE 2 OF SECOND SUBUNIT IS DELETED
Source: (gene. exp.) ENTEROBACTERIA PHAGE MS2 (virus) / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): TOP 10 / References: UniProt: P03612
Sequence detailsCOVALENT DIMER OF MS2 COAT PROTEIN SUBUNITS, SERINE 2 OF SECOND SUBUNIT IS DELETED

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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: 4.6 Å3/Da / Density % sol: 70.8 % / Description: NONE
Crystal growpH: 9 / Details: 0.1M BICINE PH 9.0, 20% PEG 5000-MONOETHYL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9814
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 10, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 4.7→50 Å / Num. obs: 72743 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 2.9
Reflection shellResolution: 4.7→4.91 Å / Redundancy: 2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.6 / % possible all: 51

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Processing

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

2ms2


Resolution: 4.7→50 Å / σ(F): 0 / Stereochemistry target values: RESIDUAL
RfactorNum. reflection% reflection
Rwork0.318 --
obs0.318 72743 84 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.99 Å2 / ksol: 0.8 e/Å3
Displacement parametersBiso mean: 105.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.78 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 4.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 0 2892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
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_deg3.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
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: 4.7→4.91 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.365 5251 -
obs--51 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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