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- PDB-9eoi: Crystal structure of the GH19 endolysin from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 9eoi
TitleCrystal structure of the GH19 endolysin from Pseudomonas aeruginosa
ComponentsPutative lytic enzyme
KeywordsCARBOHYDRATE / Endolysin / peptidoglycan / GH19
Function / homology: / Lysozyme-like domain superfamily / CITRATE ANION / Putative lytic enzyme
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsEdvardsen, P.K.T. / Englund, A.N.B. / Rohr, A.K. / Vaaje-Kolstad, G.
Funding support Norway, 1items
OrganizationGrant numberCountry
Other government Norway
CitationJournal: Biochemistry / Year: 2025
Title: Pseudomonas aeruginosa Cryptic Prophage Endolysin Is a Highly Active Muramidase.
Authors: Thoren Edvardsen, P.K. / Englund, A.N. / Kjendseth Rohr, A. / Mesnage, S. / Vaaje-Kolstad, G.
History
DepositionMar 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lytic enzyme
B: Putative lytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3304
Polymers45,9522
Non-polymers3782
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint2 kcal/mol
Surface area19660 Å2
Unit cell
Length a, b, c (Å)65.406, 79.696, 91.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Putative lytic enzyme


Mass: 22975.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: lys, PA14_08160 / Production host: Escherichia coli (E. coli) / Strain (production host): OverExpress C43(DE3) / References: UniProt: A0A0H2ZLP8
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tri-Sodium Citrate dihydrate, 15% PEG3350 / PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.77→45.82 Å / Num. obs: 47293 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 26.66 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.051 / Net I/σ(I): 10.1
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4592 / CC1/2: 0.778 / Rrim(I) all: 0.87 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→45.81 Å / SU ML: 0.2602 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2543 2320 4.92 %
Rwork0.2162 44879 -
obs0.2181 47199 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.21 Å2
Refinement stepCycle: LAST / Resolution: 1.77→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 26 267 3529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653328
X-RAY DIFFRACTIONf_angle_d0.86014524
X-RAY DIFFRACTIONf_chiral_restr0.0513473
X-RAY DIFFRACTIONf_plane_restr0.0106615
X-RAY DIFFRACTIONf_dihedral_angle_d8.2184481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.45071280.40652560X-RAY DIFFRACTION98.53
1.81-1.850.40621440.36612586X-RAY DIFFRACTION99.56
1.85-1.890.34151450.31162573X-RAY DIFFRACTION99.67
1.89-1.940.32041180.30142650X-RAY DIFFRACTION99.93
1.94-1.990.26791420.26942610X-RAY DIFFRACTION99.71
1.99-2.050.31321300.2492629X-RAY DIFFRACTION99.78
2.05-2.110.27771300.22932595X-RAY DIFFRACTION99.78
2.11-2.190.32061390.22342646X-RAY DIFFRACTION99.68
2.19-2.280.24011330.21782594X-RAY DIFFRACTION99.71
2.28-2.380.24311310.21392652X-RAY DIFFRACTION99.86
2.38-2.50.26171230.21672647X-RAY DIFFRACTION99.86
2.5-2.660.28321410.23062629X-RAY DIFFRACTION99.71
2.66-2.870.27171340.23312655X-RAY DIFFRACTION99.75
2.87-3.160.25561420.23012638X-RAY DIFFRACTION99.75
3.16-3.610.24141560.20272679X-RAY DIFFRACTION100
3.61-4.550.19841390.16962705X-RAY DIFFRACTION99.89
4.55-45.810.22291450.18122831X-RAY DIFFRACTION99.4

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