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- PDB-5ly8: Structure of the CBM2 module of Lactobacillus casei BL23 phage J-... -

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Basic information

Entry
Database: PDB / ID: 5ly8
TitleStructure of the CBM2 module of Lactobacillus casei BL23 phage J-1 evolved Dit.
ComponentsTail component
KeywordsSUGAR BINDING PROTEIN / bacteriophage infection / Lactobacillus casei / fluorescence microscopy / Carbohydrate Binding Module
Function / homologyDistal tail protein, N-terminal / : / Siphovirus-type tail component / Phage tail protein RIFT-related domain / Galactose-binding-like domain superfamily / metal ion binding / Tail component
Function and homology information
Biological speciesLactobacillus phage J-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsCambillau, C. / Spinelli, S. / Dieterle, M.-E. / Piuri, M.
CitationJournal: Mol Microbiol / Year: 2017
Title: Evolved distal tail carbohydrate binding modules of Lactobacillus phage J-1: a novel type of anti-receptor widespread among lactic acid bacteria phages.
Authors: Maria-Eugenia Dieterle / Silvia Spinelli / Irina Sadovskaya / Mariana Piuri / Christian Cambillau /
Abstract: Bacteriophage replication requires specific host-recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non-contractile tail. This baseplate holds receptor binding ...Bacteriophage replication requires specific host-recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non-contractile tail. This baseplate holds receptor binding proteins (RBPs) that can recognize the host cell-wall polysaccharide (CWPS) and specifically attach the phage to its host. While most phages possess a dedicated RBP, the phage J-1 that infects Lactobacillus casei seemed to lack one. It has been shown that the phage J-1 distal tail protein (Dit) plays a role in host recognition and that its sequence comprises two inserted modules compared with 'classical' Dits. The first insertion is similar to carbohydrate-binding modules (CBMs), whereas the second insertion remains undocumented. Here, we determined the structure of the second insertion and found it also similar to several CBMs. Expressed insertion CBM2, but not CBM1, binds to L. casei cells and neutralize phage attachment to the bacterial cell wall and the isolated and purified CWPS of L. casei BL23 prevents CBM2 attachment to the host. Electron microscopy single particle reconstruction of the J-1 virion baseplate revealed that CBM2 is projected at the periphery of Dit to optimally bind the CWPS receptor. Taken together, these results identify J-1 evolved Dit as the phage RBP.
History
DepositionSep 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7823
Polymers27,7331
Non-polymers492
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.020, 63.670, 74.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tail component


Mass: 27733.031 Da / Num. of mol.: 1 / Mutation: module residues 368-614
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus phage J-1 (virus) / Gene: J1_16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: U5U3S0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: protein at 8 mg/mL in 0.8-1.2 M sodium citrate as precipitant with 10mM sodium borate at pH 8.9-9.7.
PH range: 8.9-9.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.28→35 Å / Num. obs: 60896 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 14.03 Å2 / CC1/2: 1 / Rsym value: 0.034 / Net I/σ(I): 28.7
Reflection shellResolution: 1.28→1.31 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.93 / % possible all: 97.6

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CBM2 CsI phased

Resolution: 1.28→34.44 Å / Cor.coef. Fo:Fc: 0.9495 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.049 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.052 / SU Rfree Blow DPI: 0.051 / SU Rfree Cruickshank DPI: 0.049
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3037 5 %RANDOM
Rwork0.1836 ---
obs0.1843 60732 99.97 %-
Displacement parametersBiso mean: 20.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.1053 Å20 Å20 Å2
2---3.037 Å20 Å2
3---3.1423 Å2
Refine analyzeLuzzati coordinate error obs: 0.153 Å
Refinement stepCycle: 1 / Resolution: 1.28→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 2 317 2242
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0121987HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.212723HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d658SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes303HARMONIC5
X-RAY DIFFRACTIONt_it1987HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.88
X-RAY DIFFRACTIONt_other_torsion15.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion248SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2544SEMIHARMONIC4
LS refinement shellResolution: 1.28→1.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2171 222 5 %
Rwork0.203 4217 -
all0.2037 4439 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 35.8491 Å / Origin y: 36.8497 Å / Origin z: 30.3748 Å
111213212223313233
T-0.0279 Å20.0082 Å2-0.0022 Å2--0.0172 Å2-0.0025 Å2---0.0324 Å2
L0.8018 °2-0.1737 °2-0.1199 °2-0.3918 °2-0.0375 °2--0.7915 °2
S0.0093 Å °-0.0279 Å °0.0064 Å °-0.011 Å °-0.0282 Å °0.0162 Å °-0.007 Å °0.0842 Å °0.0189 Å °
Refinement TLS groupSelection details: { A|* }

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