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- PDB-5fs4: Bacteriophage AP205 coat protein -

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Basic information

Entry
Database: PDB / ID: 5fs4
TitleBacteriophage AP205 coat protein
ComponentsAP205 BACTERIOPHAGE COAT PROTEIN
KeywordsVIRAL PROTEIN / SMALL RNA PHAGE / COAT PROTEIN / AP205
Function / homologyviral capsid / Coat protein
Function and homology information
Biological speciesACINETOBACTER PHAGE AP205 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.73 Å
AuthorsShishovs, M. / Tars, K.
CitationJournal: J Mol Biol / Year: 2016
Title: Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages.
Authors: Mihails Shishovs / Janis Rumnieks / Christoph Diebolder / Kristaps Jaudzems / Loren B Andreas / Jan Stanek / Andris Kazaks / Svetlana Kotelovica / Inara Akopjana / Guido Pintacuda / Roman I ...Authors: Mihails Shishovs / Janis Rumnieks / Christoph Diebolder / Kristaps Jaudzems / Loren B Andreas / Jan Stanek / Andris Kazaks / Svetlana Kotelovica / Inara Akopjana / Guido Pintacuda / Roman I Koning / Kaspars Tars /
Abstract: AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus- ...AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions.
History
DepositionDec 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP205 BACTERIOPHAGE COAT PROTEIN
B: AP205 BACTERIOPHAGE COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,1502
Polymers28,1502
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-46.3 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.600, 114.930, 42.800
Angle α, β, γ (deg.)90.00, 98.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8754, 0.4026, 0.2677), (0.4028, -0.9135, 0.05679), (0.2674, 0.05811, -0.9618)
Vector: -23.01, 62.91, 66.86)

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Components

#1: Protein AP205 BACTERIOPHAGE COAT PROTEIN


Mass: 14074.790 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER PHAGE AP205 (virus) / Plasmid: PRSF-TEVDUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9AZ42
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SERINE AS A RESULT OF RECOMBINANT CONSTRUCT INSERTION IN A PLASMID

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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

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.57 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20 % ETHYLENE GLYCOL AQUEOUS SOLUTION, 7 MG/ML PROTEIN IN 40 MM TRIS-HCL PH 8,0, 300 MM NACL, VAPOR DIFFUSION SITTING DROP METHOR, 0.7 MIKROL PRECIPITANT PLUS 1 MIKROL PROTEIN,TEMPERATURE 294 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2015 / Details: MULTILAYER
RadiationMonochromator: SI CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→57.45 Å / Num. obs: 28660 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.6
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.6 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.73→57.53 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.822 / SU B: 4.263 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27454 1416 4.9 %RANDOM
Rwork0.23026 ---
obs0.23246 27197 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.587 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20.17 Å2
2---0.8 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.73→57.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 0 208 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021866
X-RAY DIFFRACTIONr_bond_other_d0.0020.021780
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9552537
X-RAY DIFFRACTIONr_angle_other_deg0.98234094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9075240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64524.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1071512
X-RAY DIFFRACTIONr_chiral_restr0.1080.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02403
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4081.343975
X-RAY DIFFRACTIONr_mcbond_other1.3521.34974
X-RAY DIFFRACTIONr_mcangle_it2.2721.9931210
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5281.474891
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.726→1.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 92 -
Rwork0.27 2009 -
obs--98.27 %

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