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- PDB-9kbs: Crystal structure of PHAb11, another peptidoglycan hydrolase with... -

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Basic information

Entry
Database: PDB / ID: 9kbs
TitleCrystal structure of PHAb11, another peptidoglycan hydrolase with thermal stability and broad-spectrum
ComponentsLysozyme
KeywordsLYASE / peptidoglycan dydrolase / cationic peptides / dimer
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / host cell cytoplasm / defense response to bacterium
Similarity search - Function
SAR-endolysin-like / Endolysin/autolysin / : / Endolysin T4 type / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsHu, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81802001 China
CitationJournal: Elife / Year: 2024
Title: Dimer-monomer transition defines a hyper-thermostable peptidoglycan hydrolase mined from bacterial proteome by lysin-derived antimicrobial peptide-primed screening.
Authors: Zhang, L. / Hu, F. / Zhao, Z. / Li, X. / Zhong, M. / He, J. / Yao, F. / Zhang, X. / Mao, Y. / Wei, H. / He, J. / Yang, H.
History
DepositionOct 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: 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.title / _citation.year
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1125
Polymers39,8362
Non-polymers2763
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.010, 54.900, 161.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Lysozyme


Mass: 19917.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Author-provided sample sequence comes from WP_038349544.1 in the NCBI database.
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: B9X95_06035 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A241ZGM3, lysozyme
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Citric acid pH 3.5, 34% v/v Polyethylene glycol 200.

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Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.27→36.62 Å / Num. obs: 21246 / % possible obs: 99.65 % / Redundancy: 12.3 % / CC1/2: 0.992 / Net I/σ(I): 14.54
Reflection shellResolution: 2.27→2.351 Å / Num. unique obs: 2049 / CC1/2: 0.747 / CC star: 0.925

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.20.1_4487refinement
xia2data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→36.62 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1052 4.96 %
Rwork0.2464 --
obs0.2475 21218 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 18 115 2388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002232
X-RAY DIFFRACTIONf_angle_d0.576312
X-RAY DIFFRACTIONf_dihedral_angle_d12.576321
X-RAY DIFFRACTIONf_chiral_restr0.037356
X-RAY DIFFRACTIONf_plane_restr0.004395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.370.35931190.29952459X-RAY DIFFRACTION100
2.37-2.50.32071240.27482509X-RAY DIFFRACTION100
2.5-2.650.27831140.26752484X-RAY DIFFRACTION100
2.65-2.860.29511530.25762460X-RAY DIFFRACTION99
2.86-3.150.3051430.24122488X-RAY DIFFRACTION100
3.15-3.60.24441432499X-RAY DIFFRACTION99
3.6-4.540.2461230.2142573X-RAY DIFFRACTION100
4.54-4.680.23541332694X-RAY DIFFRACTION100

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