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- PDB-8i2e: Crystal structure of Bacillus subtilis LytE in complex with IseA -

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Basic information

Entry
Database: PDB / ID: 8i2e
TitleCrystal structure of Bacillus subtilis LytE in complex with IseA
Components
  • Probable peptidoglycan endopeptidase LytE
  • Uncharacterized protein YoeB
KeywordsANTIMICROBIAL PROTEIN/INHIBITOR / DL-endopeptidase / ANTIMICROBIAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


lytic endotransglycosylase activity / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell wall organization / proteolysis / extracellular region
Similarity search - Function
DL-endopeptidase inhibitor IseA / IseA DL-endopeptidase inhibitor / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Uncharacterized protein YoeB / Probable peptidoglycan endopeptidase LytE
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTandukar, S. / Kwon, E. / Kim, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: Structural insights into the regulation of peptidoglycan DL-endopeptidases by inhibitory protein IseA.
Authors: Tandukar, S. / Kwon, E. / Kim, D.Y.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein YoeB
B: Probable peptidoglycan endopeptidase LytE
C: Uncharacterized protein YoeB
D: Probable peptidoglycan endopeptidase LytE


Theoretical massNumber of molelcules
Total (without water)102,0584
Polymers102,0584
Non-polymers00
Water00
1
A: Uncharacterized protein YoeB
B: Probable peptidoglycan endopeptidase LytE


Theoretical massNumber of molelcules
Total (without water)51,0292
Polymers51,0292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-6 kcal/mol
Surface area12520 Å2
MethodPISA
2
C: Uncharacterized protein YoeB
D: Probable peptidoglycan endopeptidase LytE


Theoretical massNumber of molelcules
Total (without water)51,0292
Polymers51,0292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-6 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.010, 87.010, 217.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Uncharacterized protein YoeB


Mass: 17815.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: yoeB / Production host: Escherichia coli B (bacteria) / References: UniProt: O34841
#2: Protein Probable peptidoglycan endopeptidase LytE / Gamma-D-glutamate-meso-diaminopimelate muropeptidase LytE / Minor autolysin LytE / Vegetative cell ...Gamma-D-glutamate-meso-diaminopimelate muropeptidase LytE / Minor autolysin LytE / Vegetative cell wall hydrolase LytE


Mass: 33213.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: lytE, cwlF, papQ, BSU09420 / Production host: Escherichia coli B (bacteria)
References: UniProt: P54421, Hydrolases; Acting on peptide bonds (peptidases)

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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: 2.02 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5 / Details: 25% (w/v) PEG1500, 100mM SPG buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.2→46.89 Å / Num. obs: 14448 / % possible obs: 99.5 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.091 / Net I/σ(I): 6.2
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.852 / Num. unique obs: 2547 / Rpim(I) all: 0.375 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→46.89 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 651 4.58 %
Rwork0.2337 --
obs0.2359 14201 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 0 0 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114344
X-RAY DIFFRACTIONf_angle_d1.3435874
X-RAY DIFFRACTIONf_dihedral_angle_d6.734578
X-RAY DIFFRACTIONf_chiral_restr0.073638
X-RAY DIFFRACTIONf_plane_restr0.009728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.39911230.33452652X-RAY DIFFRACTION99
3.45-3.790.41481180.31192591X-RAY DIFFRACTION96
3.79-4.340.29931360.24672657X-RAY DIFFRACTION97
4.34-5.470.22491200.19262755X-RAY DIFFRACTION99
5.47-46.890.23611540.19752895X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 27.8182 Å / Origin y: -18.2826 Å / Origin z: -0.8113 Å
111213212223313233
T0.617 Å2-0.0215 Å2-0.0694 Å2-0.6767 Å20.0324 Å2--0.6137 Å2
L0.8639 °20.2393 °20.5938 °2-0.7884 °20.4994 °2--0.8669 °2
S-0.0452 Å °-0.0633 Å °0.0625 Å °-0.0214 Å °0.0376 Å °0.0968 Å °0.0263 Å °-0.1411 Å °-0.0079 Å °
Refinement TLS groupSelection details: all

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