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- PDB-8app: AbLys1 endolysin from Acinetobacter baumannii phage AbTZA1 -

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Basic information

Entry
Database: PDB / ID: 8app
TitleAbLys1 endolysin from Acinetobacter baumannii phage AbTZA1
ComponentsEndolysin
KeywordsHYDROLASE / Endolysin / Antibacterial / Enzybiotic
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Endolysin/autolysin / : / Lysozyme - #40 / Endolysin T4 type / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesAcinetobacter phage AbTZA1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPremetis, G.E. / Stathi, A. / Papageorgiou, A.C. / Labrou, N.E.
Funding support Greece, European Union, 2items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)4036 Greece
iNEXT-Discovery13636European Union
CitationJournal: Febs J. / Year: 2023
Title: Characterization of a glycoside hydrolase endolysin from Acinetobacter baumannii phage AbTZA1 with high antibacterial potency and novel structural features.
Authors: Premetis, G.E. / Stathi, A. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionAug 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: 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: Endolysin
B: Endolysin
C: Endolysin
D: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0439
Polymers86,5714
Non-polymers4725
Water10,575587
1
C: Endolysin
hetero molecules

D: Endolysin
hetero molecules

A: Endolysin
hetero molecules

B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0439
Polymers86,5714
Non-polymers4725
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_645-x+1,y-1/2,-z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area7570 Å2
ΔGint-54 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.653, 184.777, 57.904
Angle α, β, γ (deg.)90.000, 110.690, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 21642.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage AbTZA1 (virus) / Plasmid: pETite-AbLys1-6His / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3T0IGR7, lysozyme
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.92 % / Description: Small rod-like crystals
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M Phosphate/citrate, 0.2 M lithium sulphate, pH 4.2, 20% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8266 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2022 / Details: KB mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.82→46.73 Å / Num. obs: 70067 / % possible obs: 96.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.5 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Net I/σ(I): 12.5
Reflection shellResolution: 1.82→1.88 Å / Redundancy: 3.2 % / Num. unique obs: 4406 / CC1/2: 0.424 / Rpim(I) all: 0.894 / Rrim(I) all: 1.276 / % possible all: 61.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 1.82→40.68 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3615
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 1990 2.85 %
Rwork0.2114 67957 -
obs0.2126 69947 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.61 Å2
Refinement stepCycle: LAST / Resolution: 1.82→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5926 0 26 587 6539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786050
X-RAY DIFFRACTIONf_angle_d0.948160
X-RAY DIFFRACTIONf_chiral_restr0.0539906
X-RAY DIFFRACTIONf_plane_restr0.00891049
X-RAY DIFFRACTIONf_dihedral_angle_d5.3269820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.4954720.4292578X-RAY DIFFRACTION51.19
1.87-1.920.35861420.36044773X-RAY DIFFRACTION94.48
1.92-1.970.38291490.30395036X-RAY DIFFRACTION99.87
1.97-2.040.31531450.2684981X-RAY DIFFRACTION99.98
2.04-2.110.27661540.25425074X-RAY DIFFRACTION99.94
2.11-2.190.28411450.25045043X-RAY DIFFRACTION99.9
2.19-2.290.27771490.22615065X-RAY DIFFRACTION99.94
2.29-2.420.2561460.22985057X-RAY DIFFRACTION99.9
2.42-2.570.2941490.2385020X-RAY DIFFRACTION99.96
2.57-2.760.29141500.23295097X-RAY DIFFRACTION99.98
2.76-3.040.34081460.2335016X-RAY DIFFRACTION99.98
3.04-3.480.25811490.21435071X-RAY DIFFRACTION99.9
3.48-4.390.21011470.16835046X-RAY DIFFRACTION99.94
4.39-40.680.18921470.17615100X-RAY DIFFRACTION99.73

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