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- PDB-8i2f: Crystal structure of Bacillus subtilis LytE catalytic domain in c... -

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Basic information

Entry
Database: PDB / ID: 8i2f
TitleCrystal structure of Bacillus subtilis LytE catalytic domain 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 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Lysin motif / LysM domain superfamily / LysM domain ...DL-endopeptidase inhibitor IseA / : / IseA DL-endopeptidase inhibitor / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / 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: 2.03 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
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)61,9204
Polymers61,9204
Non-polymers00
Water11,241624
1
A: Uncharacterized protein YoeB
B: Probable peptidoglycan endopeptidase LytE


Theoretical massNumber of molelcules
Total (without water)30,9602
Polymers30,9602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-9 kcal/mol
Surface area12430 Å2
MethodPISA
2
C: Uncharacterized protein YoeB
D: Probable peptidoglycan endopeptidase LytE


Theoretical massNumber of molelcules
Total (without water)30,9602
Polymers30,9602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-10 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.830, 74.640, 153.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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)
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: 13144.678 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 / Production host: Escherichia coli B (bacteria)
References: UniProt: P54421, Hydrolases; Acting on peptide bonds (peptidases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5
Details: 20% (w/v) PEG6000, 100 mM Citric acid/Sodium hydroxide pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.03→76.54 Å / Num. obs: 45047 / % possible obs: 98.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.05 / Net I/σ(I): 9.1
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3272 / Rpim(I) all: 0.305 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→76.54 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 2196 4.89 %
Rwork0.1734 --
obs0.1751 44931 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→76.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4234 0 0 624 4858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064344
X-RAY DIFFRACTIONf_angle_d0.7965874
X-RAY DIFFRACTIONf_dihedral_angle_d6.279578
X-RAY DIFFRACTIONf_chiral_restr0.052638
X-RAY DIFFRACTIONf_plane_restr0.006728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.070.26881180.22422649X-RAY DIFFRACTION98
2.07-2.120.27451510.22412611X-RAY DIFFRACTION98
2.12-2.170.24781390.21262632X-RAY DIFFRACTION98
2.17-2.230.24951290.20242631X-RAY DIFFRACTION98
2.23-2.30.23681270.19622555X-RAY DIFFRACTION95
2.3-2.370.21531340.1882645X-RAY DIFFRACTION98
2.37-2.460.23521130.19222724X-RAY DIFFRACTION99
2.46-2.560.24181570.18872652X-RAY DIFFRACTION99
2.56-2.670.24961150.18762697X-RAY DIFFRACTION98
2.67-2.810.21941270.18452590X-RAY DIFFRACTION96
2.81-2.990.24081550.19042661X-RAY DIFFRACTION98
2.99-3.220.20091520.18292711X-RAY DIFFRACTION99
3.22-3.540.20081490.16662702X-RAY DIFFRACTION99
3.54-4.060.2091490.15352667X-RAY DIFFRACTION97
4.06-5.110.14561450.13752778X-RAY DIFFRACTION99
5.11-76.540.17751360.15562830X-RAY DIFFRACTION96

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