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- PDB-8q2g: X-ray structure of LysECD7 endolysin against Gram-negative bacteria -

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Basic information

Entry
Database: PDB / ID: 8q2g
TitleX-ray structure of LysECD7 endolysin against Gram-negative bacteria
ComponentsPeptidoglycan L-alanyl-D-glutamate endopeptidase
KeywordsANTIMICROBIAL PROTEIN / Endolysins / Bacteriophage lytic enzymes / Gram-negative bacteria / Antibacterial therapy / Antimicrobial agents / ANTIBIOTIC
Function / homologyPeptidase M15C / D-alanyl-D-alanine carboxypeptidase / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / Peptidoglycan L-alanyl-D-glutamate endopeptidase
Function and homology information
Biological speciesEscherichia phage ECD7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsPrudnikova, T. / Grinkevich, P. / Vasina, D.V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biomed.Sci. / Year: 2024
Title: Development of novel antimicrobials with engineered endolysin LysECD7-SMAP to combat Gram-negative bacterial infections.
Authors: Vasina, D.V. / Antonova, N.P. / Gushchin, V.A. / Aleshkin, A.V. / Fursov, M.V. / Fursova, A.D. / Gancheva, P.G. / Grigoriev, I.V. / Grinkevich, P. / Kondratev, A.V. / Kostarnoy, A.V. / ...Authors: Vasina, D.V. / Antonova, N.P. / Gushchin, V.A. / Aleshkin, A.V. / Fursov, M.V. / Fursova, A.D. / Gancheva, P.G. / Grigoriev, I.V. / Grinkevich, P. / Kondratev, A.V. / Kostarnoy, A.V. / Lendel, A.M. / Makarov, V.V. / Nikiforova, M.A. / Pochtovyi, A.A. / Prudnikova, T. / Remizov, T.A. / Shevlyagina, N.V. / Siniavin, A.E. / Smirnova, N.S. / Terechov, A.A. / Tkachuk, A.P. / Usachev, E.V. / Vorobev, A.M. / Yakimakha, V.S. / Yudin, S.M. / Zackharova, A.A. / Zhukhovitsky, V.G. / Logunov, D.Y. / Gintsburg, A.L.
History
DepositionAug 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan L-alanyl-D-glutamate endopeptidase


Theoretical massNumber of molelcules
Total (without water)16,1171
Polymers16,1171
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.568, 82.334, 64.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

21A-244-

HOH

31A-246-

HOH

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Components

#1: Protein Peptidoglycan L-alanyl-D-glutamate endopeptidase


Mass: 16117.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage ECD7 (virus) / Gene: cwlK / Plasmid: pET42b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A220NTE5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Ammonium sulfate, 20% w/v Polyethylene glycol 3,350 pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.49→42.174 Å / Num. obs: 10864 / % possible obs: 97.4 % / Redundancy: 6 % / CC1/2: 0.99 / Net I/σ(I): 13.04
Reflection shellResolution: 2.49→2.56 Å / Num. unique obs: 3326 / CC1/2: 0.81 / % possible all: 93.83

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→42.174 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.845 / WRfactor Rfree: 0.337 / WRfactor Rwork: 0.263 / SU B: 18.5 / SU ML: 0.384 / Average fsc free: 0.6957 / Average fsc work: 0.7566 / Cross valid method: FREE R-VALUE / ESU R: 0.497 / ESU R Free: 0.383 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.358 691 9.835 %
Rwork0.2675 6335 -
all0.276 --
obs-7026 95.657 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.967 Å2
Baniso -1Baniso -2Baniso -3
1-0.324 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.036 Å2
Refinement stepCycle: LAST / Resolution: 2.49→42.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 0 46 1051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121039
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.6391401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.565125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.99121.15452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95715189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.294157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02781
X-RAY DIFFRACTIONr_nbd_refined0.2440.2535
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.244
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3920.29
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3030.22
X-RAY DIFFRACTIONr_mcbond_it3.8735.743503
X-RAY DIFFRACTIONr_mcangle_it6.0238.61627
X-RAY DIFFRACTIONr_scbond_it4.0456.075536
X-RAY DIFFRACTIONr_scangle_it6.2298.908774
X-RAY DIFFRACTIONr_lrange_it10.41876.1091619
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.49-2.5550.487580.4644290.4675190.4960.53993.83430.402
2.555-2.6250.416580.4264510.4255180.4920.4998.26260.367
2.625-2.70.464540.4034390.415010.4210.53198.40320.318
2.7-2.7830.392450.3764420.3784920.6010.51898.98370.321
2.783-2.8740.37510.3714140.3714770.5470.64297.48430.306
2.874-2.9740.386430.3094010.3174560.7320.74197.36840.265
2.974-3.0860.314540.2663790.2724490.7830.83396.43650.237
3.086-3.2110.394290.2823790.2884280.7070.82295.32710.25
3.211-3.3530.45350.2733480.294060.7010.83194.3350.258
3.353-3.5160.361300.2583640.2654080.7460.86196.56860.241
3.516-3.7050.351360.33240.3043810.8210.86994.48820.272
3.705-3.9270.354250.2753070.2813530.8180.8894.0510.262
3.927-4.1960.304350.2212850.233380.8770.91994.67460.228
4.196-4.5280.227240.1812780.1843170.9220.94195.26810.169
4.528-4.9550.278330.1852490.1962960.9220.94695.27030.181
4.955-5.530.471280.1862280.212720.8520.94394.11760.186
5.53-6.3680.456160.2172080.2312410.9030.91392.94610.215
6.368-7.7550.337190.211740.2212080.870.91592.78850.213
7.755-10.7860.188110.211480.2081720.9190.92592.44190.229
10.786-42.1740.43470.408880.411090.890.84687.1560.914

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