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- PDB-2bny: MS2 (N87A mutant) - RNA hairpin complex -

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Basic information

Entry
Database: PDB / ID: 2bny
TitleMS2 (N87A mutant) - RNA hairpin complex
Components
  • 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
  • MS2 COAT PROTEIN
KeywordsVIRUS / CAPSID / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / HAIRPIN / LEVIVIRUS / VIRUS/VIRAL PROTEIN/RNA / 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
RNA / RNA (> 10) / Capsid protein
Similarity search - Component
Biological speciesENTEROBACTERIO PHAGE MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHorn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. ...Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G.
CitationJournal: Structure / Year: 2006
Title: Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2.
Authors: Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G.
History
DepositionApr 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'


Theoretical massNumber of molelcules
Total (without water)53,2125
Polymers53,2125
Non-polymers00
Water1,53185
1
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 60


Theoretical massNumber of molelcules
Total (without water)3,192,698300
Polymers3,192,698300
Non-polymers00
Water4,324240
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: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 5


  • icosahedral pentamer
  • 266 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)266,05825
Polymers266,05825
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 6


  • icosahedral 23 hexamer
  • 319 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)319,27030
Polymers319,27030
Non-polymers00
Water43224
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: MS2 COAT PROTEIN
B: MS2 COAT PROTEIN
C: MS2 COAT PROTEIN
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
x 10


  • crystal asymmetric unit, crystal frame
  • 532 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)532,11650
Polymers532,11650
Non-polymers00
Water72140
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: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(-7.0E-6, -0.934176, 0.356813), (-0.356827, 0.33333, 0.872672), (-0.93418, -0.127331, -0.333324)
3generate(0.809013, -0.110269, 0.57734), (-0.467093, 0.475679, 0.74535), (-0.356826, -0.872687, 0.333341)
4generate(0.500003, -0.86602, -3.0E-6), (-0.645495, -0.372676, -0.666658), (0.577363, 0.333334, -0.745361)
5generate(0.499998, -0.645498, 0.577338), (-0.866031, -0.372681, 0.333333), (4.0E-6, -0.666675, -0.745351)
6generate(0.30902, -0.755754, -0.577352), (-0.755766, -0.563664, 0.333336), (-0.57735, 0.333329, -0.745356)
7generate(0.809022, -0.46708, -0.356818), (-0.110259, 0.475688, -0.872669), (0.57736, 0.745362, 0.333326)
8generate(0.809023, 0.110276, -0.577347), (-0.467084, -0.475684, -0.745347), (-0.356817, 0.872684, -0.333338)
9generate(0.309005, -0.178418, 0.934164), (0.178413, 0.975684, 0.127318), (-0.93418, 0.12732, 0.333344)
10generate(0.809013, 0.46709, 0.356821), (0.11027, 0.475686, -0.872672), (-0.57735, 0.745363, 0.333336)

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Components

#1: Protein MS2 COAT PROTEIN


Mass: 13695.438 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIO PHAGE MS2 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03612
#2: RNA chain 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *UP*AP*CP*CP*CP*AP*UP*GP*U)-3' / MS2 HAIRPIN


Mass: 6062.657 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ENTEROBACTERIO PHAGE MS2 (virus)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAINS A, B AND C: ASN 87 TO ALA

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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

CrystalDescription: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 102199 / % possible obs: 49 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.13
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.23 / % possible all: 14

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 3→27.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 13249027.85 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 979 1 %RANDOM
Rwork0.202 ---
obs0.202 102051 49.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.6639 Å2 / ksol: 0.265698 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å25.99 Å20 Å2
2--3.36 Å20 Å2
3----6.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 590 0 85 3561
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
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→3.05 Å / Rfactor Rfree error: 0.079 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 23 1.6 %
Rwork0.307 1412 -
obs--14 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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