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- PDB-7sj5: Bacteriophage lambda major capsid protein mutant - W308A -

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Basic information

Entry
Database: PDB / ID: 7sj5
TitleBacteriophage lambda major capsid protein mutant - W308A
ComponentsMajor capsid protein
KeywordsSTRUCTURAL PROTEIN / major capsid protein / HK97-fold / assembly incompetent
Function / homologyMajor capsid protein GpE / Phage major capsid protein E / T=7 icosahedral viral capsid / viral capsid / host cell cytoplasm / Major capsid protein
Function and homology information
Biological speciesEscherichia phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.695 Å
AuthorsDavis, C.R. / Churchill, M.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 2016019 United States
National Science Foundation (NSF, United States)GRFP 2016218284 United States
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Characterization of a Primordial Major Capsid-Scaffolding Protein Complex in Icosahedral Virus Shell Assembly.
Authors: Davis, C.R. / Backos, D. / Morais, M.C. / Churchill, M.E.A. / Catalano, C.E.
History
DepositionOct 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)152,4564
Polymers152,4564
Non-polymers00
Water2,936163
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein

D: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)152,4564
Polymers152,4564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_548-x+1/2,y-1/2,-z+31
Buried area8470 Å2
ΔGint-18 kcal/mol
Surface area60420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.153, 95.303, 113.121
Angle α, β, γ (deg.)90.000, 127.920, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Major capsid protein / Gene product E / gpE / Major head protein


Mass: 38114.027 Da / Num. of mol.: 4 / Mutation: W308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage lambda (virus) / Gene: E, lambdap08, gpE / Production host: Escherichia coli (E. coli) / References: UniProt: P03713
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.17 % / Description: 70 micron rhomboid prism
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1 M bis-tris, 0.1 M ammonium sulfate, 5% v/v glycerol, 30% v/v PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.695→29.75 Å / Num. obs: 39376 / % possible obs: 99.53 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.19 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05594 / Rpim(I) all: 0.0336 / Rrim(I) all: 0.06535 / Net I/av σ(I): 18.27 / Net I/σ(I): 18.27
Reflection shellResolution: 2.695→2.791 Å / Num. unique obs: 3819 / CC1/2: 0.919

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Processing

Software
NameVersionClassification
PHENIXdev-3724refinement
XDSdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BQW

3bqw


Resolution: 2.695→29.75 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 2044 -
Rwork0.2074 --
obs-39363 99.53 %
Displacement parametersBiso mean: 74.44 Å2
Refinement stepCycle: LAST / Resolution: 2.695→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10638 0 0 163 10801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210842
X-RAY DIFFRACTIONf_angle_d0.456814679
X-RAY DIFFRACTIONf_chiral_restr0.04111616
X-RAY DIFFRACTIONf_plane_restr0.00361941
X-RAY DIFFRACTIONf_dihedral_angle_d15.97724096
LS refinement shellResolution: 2.695→2.791 Å
RfactorNum. reflection% reflection
Rfree0.3087 195 -
Rwork0.2739 3819 -
obs--97.15 %

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