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- PDB-5mnt: Bacteriophage Qbeta maturation protein -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5mnt
TitleBacteriophage Qbeta maturation protein
ComponentsA2 maturation protein
KeywordsRNA BINDING PROTEIN / virus attachment / minor capsid protein
Function / homology
Function and homology information


symbiont-mediated suppression of host cell wall biogenesis / symbiont-mediated suppression of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / viral release from host cell by cytolysis / virion component
Similarity search - Function
Assembly protein / Phage maturation protein
Similarity search - Domain/homology
Maturation protein A2
Similarity search - Component
Biological speciesEnterobacteria phage Qbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.32 Å
AuthorsRumnieks, J. / Tars, K.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Crystal Structure of the Maturation Protein from Bacteriophage Q beta.
Authors: Rumnieks, J. / Tars, K.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A2 maturation protein
B: A2 maturation protein
C: A2 maturation protein
D: A2 maturation protein


Theoretical massNumber of molelcules
Total (without water)194,5044
Polymers194,5044
Non-polymers00
Water00
1
A: A2 maturation protein


Theoretical massNumber of molelcules
Total (without water)48,6261
Polymers48,6261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A2 maturation protein


Theoretical massNumber of molelcules
Total (without water)48,6261
Polymers48,6261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: A2 maturation protein


Theoretical massNumber of molelcules
Total (without water)48,6261
Polymers48,6261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: A2 maturation protein


Theoretical massNumber of molelcules
Total (without water)48,6261
Polymers48,6261
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.789, 232.515, 353.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
A2 maturation protein


Mass: 48626.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Qbeta (virus) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q8LTE2

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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: 5.97 Å3/Da / Density % sol: 79.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40 mM potassium dihydrogen phosphate, 17% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.32→176.74 Å / Num. all: 256850 / Num. obs: 67077 / % possible obs: 97.1 % / Redundancy: 3.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.176 / Net I/σ(I): 8.74
Reflection shellResolution: 3.32→3.52 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 1.42 / CC1/2: 0.518 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.32→176.74 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.88 / SU B: 32.667 / SU ML: 0.446 / Cross valid method: THROUGHOUT / ESU R: 0.994 / ESU R Free: 0.444 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27936 3335 5 %RANDOM
Rwork0.22824 ---
obs0.23073 63534 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 96.203 Å2
Baniso -1Baniso -2Baniso -3
1--6.86 Å2-0 Å20 Å2
2--5.13 Å20 Å2
3---1.72 Å2
Refinement stepCycle: 1 / Resolution: 3.32→176.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13774 0 0 0 13774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914147
X-RAY DIFFRACTIONr_bond_other_d0.0030.0213342
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.94219196
X-RAY DIFFRACTIONr_angle_other_deg0.964330434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37451676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75322.301743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.724152290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.61615152
X-RAY DIFFRACTIONr_chiral_restr0.080.22035
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116141
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023731
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_it4.3339.456716
X-RAY DIFFRACTIONr_mcbond_other4.3339.4496715
X-RAY DIFFRACTIONr_mcangle_it7.14314.1768388
X-RAY DIFFRACTIONr_mcangle_other7.14314.1778389
X-RAY DIFFRACTIONr_scbond_it4.2369.7917431
X-RAY DIFFRACTIONr_scbond_other4.2359.7917431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.28514.53110808
X-RAY DIFFRACTIONr_long_range_B_refined10.87915839
X-RAY DIFFRACTIONr_long_range_B_other10.87915840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.32→3.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 220 -
Rwork0.406 4363 -
obs--90.88 %

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