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- PDB-6su5: Ph2119 endolysin from Thermus scotoductus MAT2119 bacteriophage Ph2119 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6su5
TitlePh2119 endolysin from Thermus scotoductus MAT2119 bacteriophage Ph2119
ComponentsLysozyme
KeywordsHYDROLASE / amidase / zinc binding / cell wall degradation / endolysine
Function / homology
Function and homology information


cytolysis / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / defense response to bacterium / zinc ion binding
Similarity search - Function
Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Lysozyme
Similarity search - Component
Biological speciesThermus phage 2119 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHakansson, M. / Al-Karadaghi, S. / Plotka, M. / Kaczorowska, A.K. / Kaczorowski, T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Research Council685778 Sweden
CitationJournal: Int J Mol Sci / Year: 2020
Title: Molecular Characterization of a Novel Lytic Enzyme LysC from Clostridium intestinale URNW and Its Antibacterial Activity Mediated by Positively Charged N -Terminal Extension.
Authors: Plotka, M. / Szadkowska, M. / Hakansson, M. / Kovacic, R. / Al-Karadaghi, S. / Walse, B. / Werbowy, O. / Kaczorowska, A.K. / Kaczorowski, T.
History
DepositionSep 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1876
Polymers19,7481
Non-polymers4405
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-58 kcal/mol
Surface area7950 Å2
Unit cell
Length a, b, c (Å)31.999, 62.617, 74.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme


Mass: 19747.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage 2119 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: W0FBY3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 293 K / Method: evaporation / Details: NaKHPO4, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.17→62.7 Å / Num. obs: 50883 / % possible obs: 99.1 % / Redundancy: 4.3 % / CC1/2: 1 / Net I/σ(I): 8.1
Reflection shellResolution: 1.17→1.19 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2429 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
REFMACrefinement
PDB_EXTRACT3.25data extraction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→47.98 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.306 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.044
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 2322 5 %RANDOM
Rwork0.144 ---
obs0.1462 44081 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.03 Å2 / Biso mean: 17.216 Å2 / Biso min: 9.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2--1.29 Å20 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.2→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 23 232 1490
Biso mean--21.66 35.71 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131366
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171275
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.6471874
X-RAY DIFFRACTIONr_angle_other_deg1.5421.5782961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8045168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86720.72569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08515216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3481510
X-RAY DIFFRACTIONr_chiral_restr0.1210.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021528
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02298
X-RAY DIFFRACTIONr_rigid_bond_restr3.5832641
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 141 -
Rwork0.356 3197 -
all-3338 -
obs--95.13 %

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